Starting phenix.real_space_refine on Fri Feb 6 03:57:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ky1_62635/02_2026/9ky1_62635_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ky1_62635/02_2026/9ky1_62635.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ky1_62635/02_2026/9ky1_62635_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ky1_62635/02_2026/9ky1_62635_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ky1_62635/02_2026/9ky1_62635.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ky1_62635/02_2026/9ky1_62635.map" } resolution = 2.8 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= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 128 5.16 5 C 14322 2.51 5 N 3532 2.21 5 O 4080 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22062 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4754 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 31, 'TRANS': 567} Chain breaks: 1 Chain: "B" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 4754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4754 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 31, 'TRANS': 567} Chain breaks: 1 Chain: "D" Number of atoms: 6095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 6095 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 35, 'TRANS': 713} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.23, per 1000 atoms: 0.19 Number of scatterers: 22062 At special positions: 0 Unit cell: (123.947, 132.8, 182.601, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 128 16.00 O 4080 8.00 N 3532 7.00 C 14322 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 153 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 383 " distance=2.05 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 141 " distance=2.05 Simple disulfide: pdb=" SG CYS B 344 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 530 " - pdb=" SG CYS B 542 " distance=2.03 Simple disulfide: pdb=" SG CYS C 153 " - pdb=" SG CYS C 166 " distance=2.05 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.10 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.00 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 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " NAG-ASN " NAG A 701 " - " ASN A 182 " " NAG C 701 " - " ASN C 182 " " NAG E 1 " - " ASN A 258 " " NAG F 1 " - " ASN B 90 " " NAG G 1 " - " ASN B 432 " " NAG H 1 " - " ASN B 103 " " NAG I 1 " - " ASN B 690 " " NAG J 1 " - " ASN B 546 " " NAG K 1 " - " ASN C 258 " " NAG L 1 " - " ASN D 90 " " NAG M 1 " - " ASN D 103 " " NAG N 1 " - " ASN D 432 " " NAG O 1 " - " ASN D 546 " " NAG P 1 " - " ASN D 690 " Time building additional restraints: 1.84 Conformation dependent library (CDL) restraints added in 831.4 milliseconds 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5060 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 12 sheets defined 71.0% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 removed outlier: 3.518A pdb=" N ARG A 14 " --> pdb=" O GLY A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 25 removed outlier: 4.179A pdb=" N GLU A 25 " --> pdb=" O LEU A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 50 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 57 through 65 removed outlier: 3.559A pdb=" N GLN A 63 " --> pdb=" O PRO A 59 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 81 removed outlier: 3.841A pdb=" N MET A 71 " --> pdb=" O GLY A 67 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ILE A 72 " --> pdb=" O GLY A 68 " (cutoff:3.500A) Proline residue: A 73 - end of helix Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 99 through 108 Processing helix chain 'A' and resid 111 through 142 removed outlier: 4.004A pdb=" N GLY A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR A 128 " --> pdb=" O MET A 124 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 170 through 178 Processing helix chain 'A' and resid 194 through 213 Processing helix chain 'A' and resid 215 through 242 removed outlier: 3.642A pdb=" N LYS A 221 " --> pdb=" O GLU A 217 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N TYR A 224 " --> pdb=" O GLY A 220 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE A 225 " --> pdb=" O LYS A 221 " (cutoff:3.500A) Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 246 through 255 Processing helix chain 'A' and resid 258 through 263 Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.900A pdb=" N TRP A 268 " --> pdb=" O GLN A 264 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N LEU A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 291 Processing helix chain 'A' and resid 298 through 349 removed outlier: 3.615A pdb=" N ASP A 302 " --> pdb=" O ASN A 298 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 315 " --> pdb=" O GLY A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 371 Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 384 through 390 Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.990A pdb=" N ALA A 399 " --> pdb=" O GLY A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 409 removed outlier: 3.509A pdb=" N THR A 408 " --> pdb=" O THR A 404 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LYS A 409 " --> pdb=" O GLU A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 446 Proline residue: A 442 - end of helix Processing helix chain 'A' and resid 454 through 470 removed outlier: 3.610A pdb=" N LEU A 458 " --> pdb=" O PRO A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 475 Processing helix chain 'A' and resid 477 through 488 Processing helix chain 'A' and resid 491 through 508 removed outlier: 3.798A pdb=" N LEU A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 522 Processing helix chain 'A' and resid 527 through 536 removed outlier: 3.734A pdb=" N GLN A 531 " --> pdb=" O ASN A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 553 removed outlier: 3.957A pdb=" N PHE A 550 " --> pdb=" O PHE A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 591 removed outlier: 3.991A pdb=" N VAL A 585 " --> pdb=" O TRP A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 609 removed outlier: 5.827A pdb=" N ILE A 597 " --> pdb=" O PRO A 593 " (cutoff:3.500A) Proline residue: A 598 - end of helix removed outlier: 3.734A pdb=" N ALA A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 608 " --> pdb=" O LYS A 604 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS A 609 " --> pdb=" O LEU A 605 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 53 removed outlier: 4.236A pdb=" N ASP B 38 " --> pdb=" O HIS B 34 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LEU B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 58 through 77 removed outlier: 3.962A pdb=" N ALA B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N PHE B 72 " --> pdb=" O LYS B 68 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU B 73 " --> pdb=" O TRP B 69 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N LYS B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SER B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 90 through 100 Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.954A pdb=" N VAL B 107 " --> pdb=" O GLY B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 109 through 129 Processing helix chain 'B' and resid 147 through 155 Processing helix chain 'B' and resid 157 through 193 Proline residue: B 178 - end of helix Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 218 through 232 removed outlier: 3.735A pdb=" N LEU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE B 223 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLU B 224 " --> pdb=" O GLY B 220 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU B 232 " --> pdb=" O HIS B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 252 removed outlier: 3.881A pdb=" N ASN B 250 " --> pdb=" O ALA B 246 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 267 No H-bonds generated for 'chain 'B' and resid 265 through 267' Processing helix chain 'B' and resid 275 through 282 removed outlier: 4.266A pdb=" N SER B 280 " --> pdb=" O ASN B 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 301 Processing helix chain 'B' and resid 305 through 318 removed outlier: 3.777A pdb=" N VAL B 318 " --> pdb=" O PHE B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 removed outlier: 4.106A pdb=" N TRP B 328 " --> pdb=" O THR B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 385 removed outlier: 3.604A pdb=" N HIS B 373 " --> pdb=" O PHE B 369 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR B 385 " --> pdb=" O TYR B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 414 removed outlier: 3.705A pdb=" N GLY B 405 " --> pdb=" O HIS B 401 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N THR B 414 " --> pdb=" O LEU B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 414 through 421 Processing helix chain 'B' and resid 431 through 447 removed outlier: 3.757A pdb=" N THR B 445 " --> pdb=" O LYS B 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 465 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 498 through 502 Processing helix chain 'B' and resid 503 through 508 Processing helix chain 'B' and resid 513 through 533 removed outlier: 3.682A pdb=" N THR B 519 " --> pdb=" O TYR B 515 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N PHE B 523 " --> pdb=" O THR B 519 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N CYS B 530 " --> pdb=" O GLN B 526 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 542 Processing helix chain 'B' and resid 547 through 561 removed outlier: 3.503A pdb=" N MET B 557 " --> pdb=" O LYS B 553 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU B 560 " --> pdb=" O ASN B 556 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY B 561 " --> pdb=" O MET B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 575 removed outlier: 3.572A pdb=" N VAL B 573 " --> pdb=" O ALA B 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 588 Processing helix chain 'B' and resid 588 through 599 Processing helix chain 'B' and resid 623 through 629 removed outlier: 3.576A pdb=" N ALA B 627 " --> pdb=" O SER B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 636 through 658 Processing helix chain 'B' and resid 696 through 714 removed outlier: 5.414A pdb=" N SER B 709 " --> pdb=" O ARG B 705 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG B 710 " --> pdb=" O MET B 706 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 766 removed outlier: 3.672A pdb=" N ILE B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 17 through 29 removed outlier: 3.621A pdb=" N THR C 23 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N GLN C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 38 through 50 Processing helix chain 'C' and resid 52 through 57 Processing helix chain 'C' and resid 57 through 65 removed outlier: 3.560A pdb=" N GLN C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 69 Processing helix chain 'C' and resid 70 through 81 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 111 through 142 removed outlier: 4.025A pdb=" N GLY C 115 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N THR C 131 " --> pdb=" O LEU C 127 " (cutoff:3.500A) Processing helix chain 'C' and resid 148 through 152 Processing helix chain 'C' and resid 163 through 169 Processing helix chain 'C' and resid 170 through 178 Processing helix chain 'C' and resid 194 through 213 Processing helix chain 'C' and resid 215 through 242 removed outlier: 3.914A pdb=" N TYR C 224 " --> pdb=" O GLY C 220 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ILE C 225 " --> pdb=" O LYS C 221 " (cutoff:3.500A) Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 246 through 255 removed outlier: 3.798A pdb=" N GLY C 250 " --> pdb=" O GLY C 246 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 264 removed outlier: 4.049A pdb=" N LEU C 262 " --> pdb=" O ASN C 258 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN C 264 " --> pdb=" O THR C 260 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 279 removed outlier: 4.128A pdb=" N TRP C 268 " --> pdb=" O GLN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 292 Processing helix chain 'C' and resid 298 through 349 removed outlier: 3.634A pdb=" N ASP C 302 " --> pdb=" O ASN C 298 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N VAL C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL C 315 " --> pdb=" O GLY C 311 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL C 324 " --> pdb=" O VAL C 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 371 Processing helix chain 'C' and resid 371 through 378 Processing helix chain 'C' and resid 384 through 391 removed outlier: 3.586A pdb=" N PHE C 388 " --> pdb=" O ASP C 384 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 401 removed outlier: 4.129A pdb=" N ALA C 399 " --> pdb=" O GLY C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 402 through 409 removed outlier: 3.551A pdb=" N THR C 408 " --> pdb=" O THR C 404 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N LYS C 409 " --> pdb=" O GLU C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 446 Proline residue: C 442 - end of helix Processing helix chain 'C' and resid 454 through 471 removed outlier: 3.510A pdb=" N LEU C 458 " --> pdb=" O PRO C 454 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 475 Processing helix chain 'C' and resid 477 through 488 removed outlier: 3.594A pdb=" N SER C 487 " --> pdb=" O SER C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 491 through 508 Processing helix chain 'C' and resid 510 through 522 Processing helix chain 'C' and resid 527 through 536 removed outlier: 3.504A pdb=" N GLN C 531 " --> pdb=" O ASN C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 536 through 553 removed outlier: 3.641A pdb=" N ILE C 545 " --> pdb=" O LEU C 541 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N PHE C 550 " --> pdb=" O PHE C 546 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 591 removed outlier: 3.988A pdb=" N VAL C 585 " --> pdb=" O TRP C 581 " (cutoff:3.500A) Processing helix chain 'C' and resid 591 through 609 removed outlier: 5.003A pdb=" N ILE C 597 " --> pdb=" O PRO C 593 " (cutoff:3.500A) Proline residue: C 598 - end of helix removed outlier: 3.732A pdb=" N ALA C 601 " --> pdb=" O ILE C 597 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN C 608 " --> pdb=" O LYS C 604 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N HIS C 609 " --> pdb=" O LEU C 605 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 52 removed outlier: 3.864A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.555A pdb=" N GLN D 60 " --> pdb=" O GLU D 56 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASN D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET D 82 " --> pdb=" O THR D 78 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TYR D 83 " --> pdb=" O LEU D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.934A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN D 102 " --> pdb=" O GLN D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 4.046A pdb=" N SER D 106 " --> pdb=" O ASN D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 130 Processing helix chain 'D' and resid 146 through 155 Processing helix chain 'D' and resid 157 through 194 Proline residue: D 178 - end of helix Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 218 through 232 removed outlier: 3.786A pdb=" N LEU D 222 " --> pdb=" O SER D 218 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 277 No H-bonds generated for 'chain 'D' and resid 275 through 277' Processing helix chain 'D' and resid 278 through 283 Processing helix chain 'D' and resid 293 through 300 Processing helix chain 'D' and resid 303 through 317 Processing helix chain 'D' and resid 324 through 331 removed outlier: 3.669A pdb=" N TRP D 328 " --> pdb=" O THR D 324 " (cutoff:3.500A) Processing helix chain 'D' and resid 365 through 384 Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.734A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.630A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 465 Processing helix chain 'D' and resid 472 through 484 Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.503A pdb=" N THR D 517 " --> pdb=" O ILE D 513 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 547 through 561 removed outlier: 3.570A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 removed outlier: 3.680A pdb=" N VAL D 573 " --> pdb=" O ALA D 569 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 588 Processing helix chain 'D' and resid 588 through 599 Processing helix chain 'D' and resid 623 through 628 removed outlier: 3.742A pdb=" N ALA D 627 " --> pdb=" O SER D 623 " (cutoff:3.500A) Processing helix chain 'D' and resid 636 through 658 Processing helix chain 'D' and resid 696 through 715 removed outlier: 5.453A pdb=" N SER D 709 " --> pdb=" O ARG D 705 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ARG D 710 " --> pdb=" O MET D 706 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N PHE D 715 " --> pdb=" O ILE D 711 " (cutoff:3.500A) Processing helix chain 'D' and resid 740 through 767 removed outlier: 3.682A pdb=" N ILE D 744 " --> pdb=" O SER D 740 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 559 through 561 Processing sheet with id=AA2, first strand: chain 'B' and resid 131 through 133 Processing sheet with id=AA3, first strand: chain 'B' and resid 262 through 263 removed outlier: 6.062A pdb=" N LEU B 262 " --> pdb=" O VAL B 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 347 through 352 removed outlier: 6.425A pdb=" N ASP B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 670 through 676 removed outlier: 4.017A pdb=" N LEU B 675 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER B 680 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ASP B 693 " --> pdb=" O ALA B 687 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 670 through 676 removed outlier: 4.017A pdb=" N LEU B 675 " --> pdb=" O SER B 680 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N SER B 680 " --> pdb=" O LEU B 675 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N LYS B 619 " --> pdb=" O LEU B 725 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 559 through 561 Processing sheet with id=AA8, first strand: chain 'D' and resid 131 through 133 Processing sheet with id=AA9, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.067A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.219A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 670 through 673 removed outlier: 6.421A pdb=" N ASP D 693 " --> pdb=" O ALA D 687 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 670 through 673 1294 hydrogen bonds defined for protein. 3801 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: 3.55 Time building geometry restraints manager: 2.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.29: 3542 1.29 - 1.44: 6486 1.44 - 1.59: 12430 1.59 - 1.74: 2 1.74 - 1.89: 208 Bond restraints: 22668 Sorted by residual: bond pdb=" C VAL B 487 " pdb=" O VAL B 487 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.04e-02 9.25e+03 4.13e+01 bond pdb=" C VAL D 487 " pdb=" O VAL D 487 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.04e-02 9.25e+03 4.04e+01 bond pdb=" C ARG B 482 " pdb=" O ARG B 482 " ideal model delta sigma weight residual 1.236 1.158 0.078 1.26e-02 6.30e+03 3.84e+01 bond pdb=" CG ASP D 499 " pdb=" OD2 ASP D 499 " ideal model delta sigma weight residual 1.249 1.142 0.107 1.90e-02 2.77e+03 3.20e+01 bond pdb=" C ARG D 482 " pdb=" O ARG D 482 " ideal model delta sigma weight residual 1.236 1.165 0.071 1.26e-02 6.30e+03 3.18e+01 ... (remaining 22663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.35: 25942 2.35 - 4.70: 4774 4.70 - 7.05: 127 7.05 - 9.40: 10 9.40 - 11.76: 1 Bond angle restraints: 30854 Sorted by residual: angle pdb=" N ASN D 718 " pdb=" CA ASN D 718 " pdb=" C ASN D 718 " ideal model delta sigma weight residual 110.44 118.73 -8.29 1.20e+00 6.94e-01 4.77e+01 angle pdb=" N VAL C 592 " pdb=" CA VAL C 592 " pdb=" CB VAL C 592 " ideal model delta sigma weight residual 110.52 114.30 -3.78 6.70e-01 2.23e+00 3.18e+01 angle pdb=" C ASN A 8 " pdb=" CA ASN A 8 " pdb=" CB ASN A 8 " ideal model delta sigma weight residual 110.17 115.57 -5.40 9.90e-01 1.02e+00 2.97e+01 angle pdb=" N ASN A 182 " pdb=" CA ASN A 182 " pdb=" C ASN A 182 " ideal model delta sigma weight residual 111.39 104.02 7.37 1.38e+00 5.25e-01 2.85e+01 angle pdb=" N ASN C 182 " pdb=" CA ASN C 182 " pdb=" C ASN C 182 " ideal model delta sigma weight residual 111.54 104.31 7.23 1.36e+00 5.41e-01 2.83e+01 ... (remaining 30849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.38: 12134 17.38 - 34.76: 1131 34.76 - 52.15: 221 52.15 - 69.53: 124 69.53 - 86.91: 9 Dihedral angle restraints: 13619 sinusoidal: 5751 harmonic: 7868 Sorted by residual: dihedral pdb=" CB CYS C 153 " pdb=" SG CYS C 153 " pdb=" SG CYS C 166 " pdb=" CB CYS C 166 " ideal model delta sinusoidal sigma weight residual -86.00 -166.70 80.70 1 1.00e+01 1.00e-02 8.05e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 383 " pdb=" CB CYS A 383 " ideal model delta sinusoidal sigma weight residual -86.00 -165.18 79.18 1 1.00e+01 1.00e-02 7.80e+01 dihedral pdb=" CB CYS A 153 " pdb=" SG CYS A 153 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -159.33 73.33 1 1.00e+01 1.00e-02 6.85e+01 ... (remaining 13616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 2657 0.099 - 0.198: 756 0.198 - 0.298: 35 0.298 - 0.397: 3 0.397 - 0.496: 1 Chirality restraints: 3452 Sorted by residual: chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.21 -0.19 2.00e-02 2.50e+03 8.79e+01 chirality pdb=" C1 NAG O 2 " pdb=" O4 NAG O 1 " pdb=" C2 NAG O 2 " pdb=" O5 NAG O 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.25 -0.15 2.00e-02 2.50e+03 5.86e+01 chirality pdb=" C1 NAG P 2 " pdb=" O4 NAG P 1 " pdb=" C2 NAG P 2 " pdb=" O5 NAG P 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.26 -0.14 2.00e-02 2.50e+03 5.18e+01 ... (remaining 3449 not shown) Planarity restraints: 3890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 2 " -0.326 2.00e-02 2.50e+03 2.83e-01 1.00e+03 pdb=" C7 NAG I 2 " 0.073 2.00e-02 2.50e+03 pdb=" C8 NAG I 2 " -0.061 2.00e-02 2.50e+03 pdb=" N2 NAG I 2 " 0.501 2.00e-02 2.50e+03 pdb=" O7 NAG I 2 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG J 1 " 0.229 2.00e-02 2.50e+03 1.90e-01 4.51e+02 pdb=" C7 NAG J 1 " -0.064 2.00e-02 2.50e+03 pdb=" C8 NAG J 1 " 0.162 2.00e-02 2.50e+03 pdb=" N2 NAG J 1 " -0.313 2.00e-02 2.50e+03 pdb=" O7 NAG J 1 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG I 1 " -0.149 2.00e-02 2.50e+03 1.24e-01 1.94e+02 pdb=" C7 NAG I 1 " 0.039 2.00e-02 2.50e+03 pdb=" C8 NAG I 1 " -0.109 2.00e-02 2.50e+03 pdb=" N2 NAG I 1 " 0.204 2.00e-02 2.50e+03 pdb=" O7 NAG I 1 " 0.016 2.00e-02 2.50e+03 ... (remaining 3887 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1695 2.76 - 3.29: 25456 3.29 - 3.83: 37128 3.83 - 4.36: 48548 4.36 - 4.90: 76364 Nonbonded interactions: 189191 Sorted by model distance: nonbonded pdb=" O GLU B 75 " pdb=" OG1 THR B 78 " model vdw 2.222 3.040 nonbonded pdb=" O SER B 617 " pdb=" NH1 ARG B 697 " model vdw 2.265 3.120 nonbonded pdb=" OD1 ASN B 53 " pdb=" NE2 GLN B 340 " model vdw 2.294 3.120 nonbonded pdb=" O VAL D 226 " pdb=" OG1 THR D 229 " model vdw 2.298 3.040 nonbonded pdb=" O VAL B 226 " pdb=" OG1 THR B 229 " model vdw 2.300 3.040 ... (remaining 189186 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.650 Find NCS groups from input model: 0.300 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: 0.010 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 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 : 0.015 0.107 22703 Z= 1.058 Angle : 1.635 11.755 30950 Z= 1.220 Chirality : 0.082 0.496 3452 Planarity : 0.009 0.283 3876 Dihedral : 14.818 86.911 8532 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.14 % Favored : 94.63 % Rotamer: Outliers : 2.19 % Allowed : 12.54 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: -1.74 (0.15), residues: 2684 helix: -0.79 (0.12), residues: 1670 sheet: -1.66 (0.62), residues: 62 loop : -1.55 (0.20), residues: 952 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG B 708 TYR 0.033 0.005 TYR D 516 PHE 0.028 0.004 PHE D 715 TRP 0.051 0.005 TRP B 271 HIS 0.015 0.003 HIS D 505 Details of bonding type rmsd covalent geometry : bond 0.01477 (22668) covalent geometry : angle 1.63420 (30854) SS BOND : bond 0.02623 ( 9) SS BOND : angle 2.45144 ( 18) hydrogen bonds : bond 0.20131 ( 1286) hydrogen bonds : angle 7.56807 ( 3801) link_BETA1-4 : bond 0.00289 ( 12) link_BETA1-4 : angle 1.17761 ( 36) link_NAG-ASN : bond 0.00324 ( 14) link_NAG-ASN : angle 1.77707 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 601 time to evaluate : 0.771 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 130 ASN cc_start: 0.7546 (t0) cc_final: 0.7272 (t0) REVERT: A 146 GLU cc_start: 0.4508 (tp30) cc_final: 0.3779 (mt-10) REVERT: A 173 ASP cc_start: 0.7787 (m-30) cc_final: 0.7525 (m-30) REVERT: A 245 LYS cc_start: 0.6585 (mttt) cc_final: 0.6147 (pmtt) REVERT: A 391 GLU cc_start: 0.5869 (mm-30) cc_final: 0.5491 (mt-10) REVERT: A 421 PHE cc_start: 0.5312 (m-80) cc_final: 0.4721 (m-80) REVERT: A 423 MET cc_start: 0.7107 (ttm) cc_final: 0.6890 (tmm) REVERT: A 452 LYS cc_start: 0.5281 (mttt) cc_final: 0.5063 (tptt) REVERT: A 464 LEU cc_start: 0.4878 (mt) cc_final: 0.4455 (tp) REVERT: A 525 LYS cc_start: 0.5550 (ttpp) cc_final: 0.5331 (ttpp) REVERT: A 564 ASP cc_start: 0.3668 (t0) cc_final: 0.3443 (t70) REVERT: A 570 PHE cc_start: 0.6103 (t80) cc_final: 0.5561 (t80) REVERT: B 128 SER cc_start: 0.8283 (t) cc_final: 0.8058 (m) REVERT: B 150 GLU cc_start: 0.7403 (mm-30) cc_final: 0.6517 (tm-30) REVERT: B 152 MET cc_start: 0.8449 (mmm) cc_final: 0.8214 (mmp) REVERT: B 182 GLU cc_start: 0.7938 (mt-10) cc_final: 0.7142 (tt0) REVERT: B 221 GLN cc_start: 0.6210 (tt0) cc_final: 0.5807 (tp40) REVERT: B 259 ILE cc_start: 0.8168 (pt) cc_final: 0.7885 (pp) REVERT: B 270 MET cc_start: 0.8185 (tpp) cc_final: 0.7570 (tpp) REVERT: B 332 MET cc_start: 0.6679 (tpp) cc_final: 0.6254 (tpt) REVERT: B 376 MET cc_start: 0.6397 (ttp) cc_final: 0.6101 (ttm) REVERT: B 446 ILE cc_start: 0.8418 (mm) cc_final: 0.8212 (mm) REVERT: B 472 GLN cc_start: 0.8419 (mt0) cc_final: 0.8201 (mt0) REVERT: B 560 LEU cc_start: 0.8019 (mp) cc_final: 0.7537 (mt) REVERT: B 589 GLU cc_start: 0.6701 (mt-10) cc_final: 0.6389 (mm-30) REVERT: B 597 ASP cc_start: 0.7177 (t0) cc_final: 0.6832 (m-30) REVERT: B 625 LYS cc_start: 0.7640 (mmmt) cc_final: 0.7396 (mmtt) REVERT: B 634 GLU cc_start: 0.7781 (tt0) cc_final: 0.7529 (tt0) REVERT: B 660 ASN cc_start: 0.7483 (m110) cc_final: 0.6777 (t0) REVERT: B 668 GLU cc_start: 0.7829 (mp0) cc_final: 0.7559 (pm20) REVERT: C 15 ILE cc_start: 0.4105 (pt) cc_final: 0.3901 (pp) REVERT: C 57 ARG cc_start: 0.6834 (tpt170) cc_final: 0.6383 (tpp-160) REVERT: C 85 LEU cc_start: 0.6890 (tp) cc_final: 0.6684 (mp) REVERT: C 95 ARG cc_start: 0.5407 (tpt90) cc_final: 0.4728 (tmt170) REVERT: C 187 ILE cc_start: 0.6120 (tt) cc_final: 0.5346 (tp) REVERT: C 216 ILE cc_start: 0.4372 (pp) cc_final: 0.4162 (tp) REVERT: C 230 PRO cc_start: 0.4888 (Cg_exo) cc_final: 0.4512 (Cg_endo) REVERT: C 268 TRP cc_start: 0.5281 (m100) cc_final: 0.4923 (m100) REVERT: C 331 GLN cc_start: 0.6049 (tp40) cc_final: 0.5514 (tm130) REVERT: C 472 ILE cc_start: 0.5751 (mm) cc_final: 0.5488 (mm) REVERT: C 481 TRP cc_start: 0.6283 (m100) cc_final: 0.5282 (m100) REVERT: C 499 PHE cc_start: 0.5164 (t80) cc_final: 0.4600 (t80) REVERT: C 535 ARG cc_start: 0.5098 (mtt-85) cc_final: 0.4369 (ttp80) REVERT: C 542 MET cc_start: 0.4988 (mtm) cc_final: 0.4762 (tmm) REVERT: C 570 PHE cc_start: 0.5518 (t80) cc_final: 0.5126 (t80) REVERT: D 41 TYR cc_start: 0.6819 (t80) cc_final: 0.6545 (t80) REVERT: D 128 SER cc_start: 0.8304 (t) cc_final: 0.8034 (m) REVERT: D 150 GLU cc_start: 0.7324 (mm-30) cc_final: 0.6491 (tm-30) REVERT: D 152 MET cc_start: 0.8377 (mmm) cc_final: 0.7718 (mmp) REVERT: D 221 GLN cc_start: 0.6460 (tt0) cc_final: 0.5608 (tp-100) REVERT: D 224 GLU cc_start: 0.7313 (mp0) cc_final: 0.6422 (pt0) REVERT: D 259 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7821 (pp) REVERT: D 270 MET cc_start: 0.8426 (mmt) cc_final: 0.5881 (tpp) REVERT: D 282 THR cc_start: 0.8063 (m) cc_final: 0.7709 (p) REVERT: D 332 MET cc_start: 0.6949 (OUTLIER) cc_final: 0.6410 (tpp) REVERT: D 472 GLN cc_start: 0.8043 (mt0) cc_final: 0.7823 (mt0) REVERT: D 474 MET cc_start: 0.8190 (mmp) cc_final: 0.7947 (mmm) REVERT: D 481 LYS cc_start: 0.8004 (OUTLIER) cc_final: 0.7637 (tptt) REVERT: D 579 MET cc_start: 0.8176 (ptm) cc_final: 0.7855 (ptp) REVERT: D 634 GLU cc_start: 0.7814 (tt0) cc_final: 0.7554 (tt0) REVERT: D 660 ASN cc_start: 0.7639 (m-40) cc_final: 0.7024 (t0) REVERT: D 668 GLU cc_start: 0.7799 (mp0) cc_final: 0.7526 (pm20) REVERT: D 713 ASP cc_start: 0.7860 (p0) cc_final: 0.7385 (m-30) outliers start: 52 outliers final: 13 residues processed: 634 average time/residue: 0.5414 time to fit residues: 393.9354 Evaluate side-chains 329 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 313 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 50 TYR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 463 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain C residue 336 CYS Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain D residue 332 MET Chi-restraints excluded: chain D residue 463 VAL Chi-restraints excluded: chain D residue 481 LYS Chi-restraints excluded: chain D residue 744 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN ** A 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 194 GLN A 274 GLN A 293 ASN A 364 GLN A 444 GLN A 476 ASN B 134 ASN B 194 ASN B 388 GLN B 401 HIS B 531 GLN B 712 ASN C 142 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 293 ASN C 377 GLN ** C 531 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 574 GLN D 76 GLN D 89 GLN D 101 GLN D 134 ASN D 159 ASN D 194 ASN D 401 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.217760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.189919 restraints weight = 25403.092| |-----------------------------------------------------------------------------| r_work (start): 0.4125 rms_B_bonded: 1.24 r_work: 0.3806 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 22703 Z= 0.177 Angle : 0.699 13.409 30950 Z= 0.356 Chirality : 0.046 0.456 3452 Planarity : 0.005 0.050 3876 Dihedral : 5.896 59.282 3479 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.09 % Favored : 96.83 % Rotamer: Outliers : 4.08 % Allowed : 18.06 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.31 (0.16), residues: 2684 helix: 0.81 (0.12), residues: 1738 sheet: -0.60 (0.60), residues: 78 loop : -0.83 (0.21), residues: 868 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 97 TYR 0.019 0.002 TYR A 128 PHE 0.020 0.002 PHE D 523 TRP 0.019 0.002 TRP D 271 HIS 0.011 0.001 HIS D 540 Details of bonding type rmsd covalent geometry : bond 0.00378 (22668) covalent geometry : angle 0.68413 (30854) SS BOND : bond 0.00682 ( 9) SS BOND : angle 1.81889 ( 18) hydrogen bonds : bond 0.05671 ( 1286) hydrogen bonds : angle 5.13399 ( 3801) link_BETA1-4 : bond 0.00573 ( 12) link_BETA1-4 : angle 1.60797 ( 36) link_NAG-ASN : bond 0.02545 ( 14) link_NAG-ASN : angle 3.54335 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 334 time to evaluate : 0.814 Fit side-chains revert: symmetry clash REVERT: A 14 ARG cc_start: 0.3657 (OUTLIER) cc_final: 0.3337 (mpp80) REVERT: A 42 MET cc_start: 0.5113 (mmm) cc_final: 0.4701 (tpt) REVERT: A 146 GLU cc_start: 0.4780 (tp30) cc_final: 0.4359 (mt-10) REVERT: A 255 PHE cc_start: 0.7188 (m-80) cc_final: 0.6830 (m-80) REVERT: A 309 ILE cc_start: 0.7211 (mt) cc_final: 0.6796 (pt) REVERT: A 432 MET cc_start: 0.7534 (mmm) cc_final: 0.7312 (mmm) REVERT: A 464 LEU cc_start: 0.6316 (mt) cc_final: 0.6080 (tp) REVERT: B 82 MET cc_start: 0.2224 (pmm) cc_final: 0.1740 (ppp) REVERT: B 152 MET cc_start: 0.9176 (mmm) cc_final: 0.8858 (mmp) REVERT: B 560 LEU cc_start: 0.8830 (mp) cc_final: 0.8469 (mt) REVERT: C 137 MET cc_start: 0.5557 (OUTLIER) cc_final: 0.5318 (ttp) REVERT: C 187 ILE cc_start: 0.5298 (tt) cc_final: 0.4714 (tp) REVERT: D 192 ARG cc_start: 0.7646 (OUTLIER) cc_final: 0.7414 (mtt180) REVERT: D 323 MET cc_start: 0.7565 (tpt) cc_final: 0.7343 (tpp) REVERT: D 327 PHE cc_start: 0.5323 (OUTLIER) cc_final: 0.5067 (t80) REVERT: D 552 GLN cc_start: 0.6929 (OUTLIER) cc_final: 0.6721 (tp40) outliers start: 97 outliers final: 36 residues processed: 408 average time/residue: 0.5494 time to fit residues: 258.0499 Evaluate side-chains 279 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ARG Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 383 CYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain B residue 762 PHE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 137 MET Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 588 ILE Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 192 ARG Chi-restraints excluded: chain D residue 327 PHE Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 552 GLN Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain D residue 750 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 83 optimal weight: 2.9990 chunk 202 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 98 optimal weight: 0.8980 chunk 238 optimal weight: 0.5980 chunk 169 optimal weight: 6.9990 chunk 195 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 27 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 217 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 130 ASN A 142 ASN B 159 ASN B 194 ASN B 580 ASN B 586 ASN C 94 GLN C 108 HIS C 130 ASN C 331 GLN D 51 ASN D 89 GLN D 134 ASN D 194 ASN D 221 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.210953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.176700 restraints weight = 25121.554| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 1.53 r_work: 0.3704 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3659 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3659 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.4204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22703 Z= 0.190 Angle : 0.692 9.853 30950 Z= 0.354 Chirality : 0.047 0.451 3452 Planarity : 0.005 0.046 3876 Dihedral : 5.639 59.291 3457 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.46 % Favored : 96.50 % Rotamer: Outliers : 4.67 % Allowed : 18.39 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 0.62 (0.16), residues: 2684 helix: 1.06 (0.12), residues: 1700 sheet: -0.16 (0.68), residues: 66 loop : -0.68 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 273 TYR 0.021 0.002 TYR A 128 PHE 0.025 0.002 PHE D 523 TRP 0.054 0.002 TRP A 534 HIS 0.008 0.002 HIS A 108 Details of bonding type rmsd covalent geometry : bond 0.00429 (22668) covalent geometry : angle 0.68130 (30854) SS BOND : bond 0.00760 ( 9) SS BOND : angle 1.95233 ( 18) hydrogen bonds : bond 0.05513 ( 1286) hydrogen bonds : angle 4.91084 ( 3801) link_BETA1-4 : bond 0.00445 ( 12) link_BETA1-4 : angle 1.45648 ( 36) link_NAG-ASN : bond 0.00403 ( 14) link_NAG-ASN : angle 2.87083 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 307 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 309 ILE cc_start: 0.7291 (mt) cc_final: 0.6839 (pt) REVERT: A 313 THR cc_start: 0.6938 (OUTLIER) cc_final: 0.6454 (t) REVERT: A 410 MET cc_start: 0.6951 (mtp) cc_final: 0.6572 (mtm) REVERT: A 432 MET cc_start: 0.7422 (mmm) cc_final: 0.7212 (mmm) REVERT: B 82 MET cc_start: 0.2394 (pmm) cc_final: 0.1837 (ppp) REVERT: B 152 MET cc_start: 0.9103 (mmm) cc_final: 0.8811 (mmp) REVERT: B 441 LYS cc_start: 0.8947 (OUTLIER) cc_final: 0.8076 (tppp) REVERT: B 552 GLN cc_start: 0.7080 (OUTLIER) cc_final: 0.6766 (tp40) REVERT: B 560 LEU cc_start: 0.8877 (mp) cc_final: 0.8452 (mt) REVERT: B 713 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7855 (m-30) REVERT: C 104 TRP cc_start: 0.5534 (m100) cc_final: 0.4999 (m100) REVERT: C 325 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7799 (mp) REVERT: C 452 LYS cc_start: 0.5191 (OUTLIER) cc_final: 0.4663 (tptt) REVERT: C 464 LEU cc_start: 0.6338 (mt) cc_final: 0.6095 (tp) REVERT: D 136 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7092 (m-30) REVERT: D 393 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.6809 (mtp85) outliers start: 111 outliers final: 39 residues processed: 387 average time/residue: 0.5061 time to fit residues: 226.1624 Evaluate side-chains 291 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 244 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 313 THR Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 439 LEU Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 552 GLN Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 713 ASP Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 248 THR Chi-restraints excluded: chain C residue 313 THR Chi-restraints excluded: chain C residue 325 ILE Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 603 TYR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 358 ILE Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 439 LEU Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 744 ILE Chi-restraints excluded: chain D residue 750 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 135 optimal weight: 20.0000 chunk 258 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 242 optimal weight: 0.9990 chunk 229 optimal weight: 0.6980 chunk 148 optimal weight: 4.9990 chunk 262 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 241 optimal weight: 0.9990 chunk 5 optimal weight: 10.0000 chunk 142 optimal weight: 10.0000 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN B 221 GLN D 51 ASN D 89 GLN D 117 ASN D 134 ASN D 194 ASN D 221 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.212306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.178125 restraints weight = 25150.920| |-----------------------------------------------------------------------------| r_work (start): 0.3986 rms_B_bonded: 1.47 r_work: 0.3708 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3667 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22703 Z= 0.140 Angle : 0.617 10.887 30950 Z= 0.311 Chirality : 0.044 0.483 3452 Planarity : 0.004 0.052 3876 Dihedral : 4.993 56.939 3452 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 4.04 % Allowed : 20.83 % Favored : 75.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 0.84 (0.16), residues: 2684 helix: 1.21 (0.12), residues: 1700 sheet: 0.07 (0.68), residues: 66 loop : -0.55 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 393 TYR 0.021 0.001 TYR A 128 PHE 0.024 0.002 PHE C 549 TRP 0.019 0.001 TRP A 534 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00305 (22668) covalent geometry : angle 0.60299 (30854) SS BOND : bond 0.00808 ( 9) SS BOND : angle 1.87746 ( 18) hydrogen bonds : bond 0.04814 ( 1286) hydrogen bonds : angle 4.74301 ( 3801) link_BETA1-4 : bond 0.00379 ( 12) link_BETA1-4 : angle 1.35342 ( 36) link_NAG-ASN : bond 0.00686 ( 14) link_NAG-ASN : angle 3.28570 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 369 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 273 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 77 LEU cc_start: 0.6973 (OUTLIER) cc_final: 0.6717 (mp) REVERT: A 119 MET cc_start: 0.6256 (ttp) cc_final: 0.5946 (ttm) REVERT: A 129 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.6541 (t80) REVERT: A 410 MET cc_start: 0.6977 (mtp) cc_final: 0.6614 (mtm) REVERT: A 502 MET cc_start: 0.4645 (mmt) cc_final: 0.4199 (mtp) REVERT: B 82 MET cc_start: 0.2436 (pmm) cc_final: 0.1904 (ppp) REVERT: B 152 MET cc_start: 0.9095 (mmm) cc_final: 0.8842 (mmp) REVERT: B 401 HIS cc_start: 0.8943 (OUTLIER) cc_final: 0.8582 (t-90) REVERT: B 560 LEU cc_start: 0.8877 (mp) cc_final: 0.8465 (mt) REVERT: C 104 TRP cc_start: 0.5740 (m100) cc_final: 0.5029 (m100) REVERT: C 270 ASP cc_start: 0.4989 (m-30) cc_final: 0.4743 (m-30) REVERT: C 452 LYS cc_start: 0.4897 (OUTLIER) cc_final: 0.4464 (tptt) REVERT: C 464 LEU cc_start: 0.6314 (mt) cc_final: 0.6064 (tp) REVERT: D 62 MET cc_start: 0.6074 (ptm) cc_final: 0.5581 (ptm) REVERT: D 393 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.6681 (mtp85) REVERT: D 401 HIS cc_start: 0.8887 (OUTLIER) cc_final: 0.8560 (t-90) REVERT: D 441 LYS cc_start: 0.9031 (OUTLIER) cc_final: 0.8344 (tptm) outliers start: 96 outliers final: 39 residues processed: 339 average time/residue: 0.4978 time to fit residues: 195.9166 Evaluate side-chains 285 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 239 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 455 LYS Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 79 VAL Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 390 SER Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 603 TYR Chi-restraints excluded: chain D residue 96 GLN Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 531 GLN Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 750 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 103 optimal weight: 0.5980 chunk 142 optimal weight: 10.0000 chunk 121 optimal weight: 0.9990 chunk 171 optimal weight: 0.0470 chunk 238 optimal weight: 0.8980 chunk 166 optimal weight: 0.9980 chunk 209 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 240 optimal weight: 3.9990 chunk 153 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 GLN B 117 ASN ** C 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 63 ASN D 89 GLN D 117 ASN D 134 ASN D 194 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.212640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.178912 restraints weight = 24977.977| |-----------------------------------------------------------------------------| r_work (start): 0.3992 rms_B_bonded: 1.51 r_work: 0.3711 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3666 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 22703 Z= 0.125 Angle : 0.599 11.370 30950 Z= 0.300 Chirality : 0.043 0.579 3452 Planarity : 0.004 0.050 3876 Dihedral : 4.828 57.292 3450 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.13 % Favored : 96.83 % Rotamer: Outliers : 4.25 % Allowed : 20.96 % Favored : 74.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 1.00 (0.16), residues: 2684 helix: 1.33 (0.13), residues: 1702 sheet: 0.02 (0.67), residues: 66 loop : -0.46 (0.21), residues: 916 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 177 TYR 0.023 0.001 TYR C 209 PHE 0.024 0.001 PHE C 549 TRP 0.042 0.001 TRP A 534 HIS 0.008 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00267 (22668) covalent geometry : angle 0.58301 (30854) SS BOND : bond 0.00884 ( 9) SS BOND : angle 2.23697 ( 18) hydrogen bonds : bond 0.04502 ( 1286) hydrogen bonds : angle 4.61577 ( 3801) link_BETA1-4 : bond 0.00373 ( 12) link_BETA1-4 : angle 1.25467 ( 36) link_NAG-ASN : bond 0.00706 ( 14) link_NAG-ASN : angle 3.33670 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 256 time to evaluate : 0.737 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 77 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6748 (mp) REVERT: A 119 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5950 (ttm) REVERT: A 129 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.6548 (t80) REVERT: A 410 MET cc_start: 0.7016 (mtp) cc_final: 0.6649 (mtm) REVERT: A 421 PHE cc_start: 0.6761 (m-80) cc_final: 0.6530 (m-80) REVERT: A 432 MET cc_start: 0.7552 (mmm) cc_final: 0.7261 (mmm) REVERT: B 62 MET cc_start: 0.4430 (OUTLIER) cc_final: 0.4110 (ttp) REVERT: B 82 MET cc_start: 0.2522 (pmm) cc_final: 0.2022 (ppp) REVERT: B 152 MET cc_start: 0.9085 (mmm) cc_final: 0.8842 (mmp) REVERT: B 401 HIS cc_start: 0.8908 (OUTLIER) cc_final: 0.8547 (t-90) REVERT: B 441 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8135 (tppp) REVERT: C 452 LYS cc_start: 0.4839 (OUTLIER) cc_final: 0.4457 (tptt) REVERT: D 62 MET cc_start: 0.6032 (ptm) cc_final: 0.5643 (ptm) REVERT: D 136 ASP cc_start: 0.7503 (OUTLIER) cc_final: 0.6940 (m-30) REVERT: D 332 MET cc_start: 0.6531 (tpp) cc_final: 0.6184 (tpt) REVERT: D 376 MET cc_start: 0.8275 (ttm) cc_final: 0.7893 (ttm) REVERT: D 401 HIS cc_start: 0.8820 (OUTLIER) cc_final: 0.8436 (t-90) REVERT: D 441 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8304 (tptm) outliers start: 101 outliers final: 39 residues processed: 324 average time/residue: 0.5222 time to fit residues: 195.7292 Evaluate side-chains 279 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LEU Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 414 THR Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 24 ILE Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 133 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 603 TYR Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 750 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 211 optimal weight: 0.0870 chunk 240 optimal weight: 0.9980 chunk 263 optimal weight: 0.9990 chunk 217 optimal weight: 0.3980 chunk 241 optimal weight: 2.9990 chunk 56 optimal weight: 50.0000 chunk 57 optimal weight: 7.9990 chunk 180 optimal weight: 20.0000 chunk 78 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 251 optimal weight: 3.9990 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 476 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 117 ASN B 221 GLN C 274 GLN D 51 ASN D 89 GLN D 117 ASN D 134 ASN D 194 ASN D 221 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.210450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.176205 restraints weight = 24985.299| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.52 r_work: 0.3702 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3656 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.4959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 22703 Z= 0.133 Angle : 0.603 10.381 30950 Z= 0.301 Chirality : 0.043 0.501 3452 Planarity : 0.004 0.043 3876 Dihedral : 4.767 56.961 3450 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 4.17 % Allowed : 21.30 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.07 (0.16), residues: 2684 helix: 1.36 (0.13), residues: 1700 sheet: 0.02 (0.66), residues: 66 loop : -0.37 (0.21), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 98 TYR 0.023 0.001 TYR A 128 PHE 0.022 0.001 PHE A 520 TRP 0.032 0.002 TRP C 268 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00297 (22668) covalent geometry : angle 0.58683 (30854) SS BOND : bond 0.00685 ( 9) SS BOND : angle 1.91077 ( 18) hydrogen bonds : bond 0.04547 ( 1286) hydrogen bonds : angle 4.60309 ( 3801) link_BETA1-4 : bond 0.00354 ( 12) link_BETA1-4 : angle 1.36533 ( 36) link_NAG-ASN : bond 0.00525 ( 14) link_NAG-ASN : angle 3.41075 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 242 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 MET cc_start: 0.6323 (ttp) cc_final: 0.6017 (ttm) REVERT: A 129 TYR cc_start: 0.7186 (OUTLIER) cc_final: 0.6263 (t80) REVERT: A 223 VAL cc_start: 0.6596 (OUTLIER) cc_final: 0.6357 (t) REVERT: A 421 PHE cc_start: 0.6772 (m-80) cc_final: 0.6565 (m-80) REVERT: A 432 MET cc_start: 0.7517 (mmm) cc_final: 0.7301 (mmm) REVERT: A 569 GLU cc_start: 0.5339 (OUTLIER) cc_final: 0.4912 (mp0) REVERT: B 53 ASN cc_start: 0.5486 (t0) cc_final: 0.5220 (m-40) REVERT: B 82 MET cc_start: 0.2111 (pmm) cc_final: 0.1662 (ppp) REVERT: B 152 MET cc_start: 0.9083 (mmm) cc_final: 0.8833 (mmp) REVERT: B 197 GLU cc_start: 0.8060 (tt0) cc_final: 0.7742 (mt-10) REVERT: B 401 HIS cc_start: 0.8936 (OUTLIER) cc_final: 0.8573 (t-90) REVERT: B 441 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8138 (tppp) REVERT: C 83 ILE cc_start: 0.6463 (OUTLIER) cc_final: 0.6118 (mt) REVERT: C 423 MET cc_start: 0.7112 (OUTLIER) cc_final: 0.6837 (ttm) REVERT: C 436 MET cc_start: 0.6605 (OUTLIER) cc_final: 0.5918 (ttm) REVERT: C 452 LYS cc_start: 0.4743 (OUTLIER) cc_final: 0.4409 (tptt) REVERT: C 483 SER cc_start: 0.7598 (OUTLIER) cc_final: 0.7279 (p) REVERT: D 62 MET cc_start: 0.6019 (ptm) cc_final: 0.5625 (ptm) REVERT: D 136 ASP cc_start: 0.7496 (OUTLIER) cc_final: 0.7090 (m-30) REVERT: D 194 ASN cc_start: 0.7944 (OUTLIER) cc_final: 0.7535 (m110) REVERT: D 376 MET cc_start: 0.8297 (ttm) cc_final: 0.7967 (ttm) REVERT: D 401 HIS cc_start: 0.8873 (OUTLIER) cc_final: 0.8509 (t-90) REVERT: D 441 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8298 (tptm) outliers start: 99 outliers final: 45 residues processed: 316 average time/residue: 0.5083 time to fit residues: 186.8212 Evaluate side-chains 282 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 223 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 239 ILE Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 SER Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 556 ASN Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 626 SER Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 603 TYR Chi-restraints excluded: chain D residue 82 MET Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 194 ASN Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 360 MET Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 750 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 52 optimal weight: 6.9990 chunk 134 optimal weight: 0.5980 chunk 168 optimal weight: 2.9990 chunk 220 optimal weight: 3.9990 chunk 136 optimal weight: 10.0000 chunk 259 optimal weight: 1.9990 chunk 263 optimal weight: 0.0980 chunk 212 optimal weight: 0.0980 chunk 262 optimal weight: 0.7980 chunk 43 optimal weight: 0.0000 chunk 174 optimal weight: 4.9990 overall best weight: 0.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 ASN D 51 ASN D 89 GLN D 117 ASN D 134 ASN D 194 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.213248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.178843 restraints weight = 25118.510| |-----------------------------------------------------------------------------| r_work (start): 0.3989 rms_B_bonded: 1.48 r_work: 0.3720 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 22703 Z= 0.119 Angle : 0.595 12.545 30950 Z= 0.293 Chirality : 0.041 0.304 3452 Planarity : 0.004 0.036 3876 Dihedral : 4.805 57.717 3450 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.98 % Favored : 96.94 % Rotamer: Outliers : 2.99 % Allowed : 23.06 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 1.18 (0.16), residues: 2684 helix: 1.46 (0.13), residues: 1692 sheet: -0.01 (0.66), residues: 66 loop : -0.33 (0.21), residues: 926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 98 TYR 0.024 0.001 TYR B 50 PHE 0.027 0.001 PHE C 570 TRP 0.064 0.001 TRP A 534 HIS 0.019 0.001 HIS D 195 Details of bonding type rmsd covalent geometry : bond 0.00246 (22668) covalent geometry : angle 0.57641 (30854) SS BOND : bond 0.01008 ( 9) SS BOND : angle 1.49269 ( 18) hydrogen bonds : bond 0.04133 ( 1286) hydrogen bonds : angle 4.51626 ( 3801) link_BETA1-4 : bond 0.00342 ( 12) link_BETA1-4 : angle 1.29504 ( 36) link_NAG-ASN : bond 0.00697 ( 14) link_NAG-ASN : angle 3.84171 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 242 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.6156 (tpp) cc_final: 0.5860 (mmp) REVERT: A 119 MET cc_start: 0.6283 (OUTLIER) cc_final: 0.6010 (ttm) REVERT: A 129 TYR cc_start: 0.6957 (OUTLIER) cc_final: 0.6111 (t80) REVERT: A 193 ILE cc_start: 0.5480 (OUTLIER) cc_final: 0.5278 (pt) REVERT: A 198 LEU cc_start: 0.6340 (OUTLIER) cc_final: 0.6035 (mt) REVERT: A 223 VAL cc_start: 0.6508 (OUTLIER) cc_final: 0.6266 (t) REVERT: A 421 PHE cc_start: 0.6698 (m-80) cc_final: 0.6486 (m-80) REVERT: A 464 LEU cc_start: 0.6301 (tm) cc_final: 0.5579 (mm) REVERT: A 569 GLU cc_start: 0.5400 (OUTLIER) cc_final: 0.5000 (mp0) REVERT: B 53 ASN cc_start: 0.5419 (t0) cc_final: 0.5165 (m-40) REVERT: B 82 MET cc_start: 0.2120 (pmm) cc_final: 0.1573 (ppp) REVERT: B 152 MET cc_start: 0.9088 (mmm) cc_final: 0.8829 (mmp) REVERT: B 197 GLU cc_start: 0.8033 (tt0) cc_final: 0.7719 (mt-10) REVERT: B 401 HIS cc_start: 0.8866 (OUTLIER) cc_final: 0.8502 (t-90) REVERT: B 441 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8142 (tppp) REVERT: B 560 LEU cc_start: 0.8754 (mt) cc_final: 0.8492 (mt) REVERT: C 83 ILE cc_start: 0.6367 (OUTLIER) cc_final: 0.6061 (mt) REVERT: C 452 LYS cc_start: 0.4777 (OUTLIER) cc_final: 0.4456 (tptt) REVERT: D 45 LEU cc_start: 0.7823 (OUTLIER) cc_final: 0.7566 (mm) REVERT: D 62 MET cc_start: 0.6017 (ptm) cc_final: 0.5628 (ptm) REVERT: D 136 ASP cc_start: 0.7386 (OUTLIER) cc_final: 0.6960 (m-30) REVERT: D 197 GLU cc_start: 0.7967 (tt0) cc_final: 0.7590 (mt-10) REVERT: D 332 MET cc_start: 0.6605 (tpp) cc_final: 0.6130 (tpt) REVERT: D 376 MET cc_start: 0.8324 (ttm) cc_final: 0.7968 (ttm) REVERT: D 401 HIS cc_start: 0.8768 (OUTLIER) cc_final: 0.8406 (t-90) outliers start: 71 outliers final: 34 residues processed: 296 average time/residue: 0.5548 time to fit residues: 189.9951 Evaluate side-chains 268 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 221 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 569 GLU Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 744 ILE Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 603 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 556 ASN Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 750 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 155 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 208 optimal weight: 2.9990 chunk 96 optimal weight: 0.4980 chunk 233 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 117 ASN ** C 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 51 ASN D 89 GLN D 531 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.210812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.170425 restraints weight = 24849.494| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 2.11 r_work: 0.3584 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.5205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22703 Z= 0.121 Angle : 0.587 10.149 30950 Z= 0.295 Chirality : 0.042 0.369 3452 Planarity : 0.004 0.063 3876 Dihedral : 4.640 57.258 3450 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 3.07 % Allowed : 23.23 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 1.20 (0.16), residues: 2684 helix: 1.47 (0.13), residues: 1704 sheet: 0.04 (0.66), residues: 66 loop : -0.33 (0.21), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 98 TYR 0.024 0.001 TYR A 128 PHE 0.025 0.001 PHE C 570 TRP 0.092 0.002 TRP A 534 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00263 (22668) covalent geometry : angle 0.57556 (30854) SS BOND : bond 0.00742 ( 9) SS BOND : angle 1.68343 ( 18) hydrogen bonds : bond 0.04235 ( 1286) hydrogen bonds : angle 4.50580 ( 3801) link_BETA1-4 : bond 0.00344 ( 12) link_BETA1-4 : angle 1.25207 ( 36) link_NAG-ASN : bond 0.00602 ( 14) link_NAG-ASN : angle 2.90358 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 229 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.6146 (tpp) cc_final: 0.5770 (mmp) REVERT: A 119 MET cc_start: 0.6513 (OUTLIER) cc_final: 0.6195 (ttm) REVERT: A 129 TYR cc_start: 0.7036 (OUTLIER) cc_final: 0.6148 (t80) REVERT: A 193 ILE cc_start: 0.5615 (OUTLIER) cc_final: 0.5344 (pt) REVERT: A 198 LEU cc_start: 0.6540 (OUTLIER) cc_final: 0.6232 (mt) REVERT: A 223 VAL cc_start: 0.6469 (OUTLIER) cc_final: 0.6235 (t) REVERT: A 421 PHE cc_start: 0.6843 (m-80) cc_final: 0.6611 (m-80) REVERT: B 53 ASN cc_start: 0.5505 (t0) cc_final: 0.5160 (m-40) REVERT: B 82 MET cc_start: 0.2257 (pmm) cc_final: 0.1671 (ppp) REVERT: B 152 MET cc_start: 0.9104 (mmm) cc_final: 0.8858 (mmp) REVERT: B 197 GLU cc_start: 0.8213 (tt0) cc_final: 0.7894 (mt-10) REVERT: B 401 HIS cc_start: 0.8907 (OUTLIER) cc_final: 0.8543 (t-90) REVERT: B 441 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8212 (tppp) REVERT: B 560 LEU cc_start: 0.8805 (mt) cc_final: 0.8543 (mt) REVERT: C 83 ILE cc_start: 0.6542 (OUTLIER) cc_final: 0.6157 (mt) REVERT: C 100 SER cc_start: 0.5850 (OUTLIER) cc_final: 0.5456 (p) REVERT: C 436 MET cc_start: 0.6852 (OUTLIER) cc_final: 0.6144 (ttm) REVERT: C 452 LYS cc_start: 0.4812 (OUTLIER) cc_final: 0.4489 (tptt) REVERT: C 545 ILE cc_start: 0.6144 (mm) cc_final: 0.5750 (mt) REVERT: D 62 MET cc_start: 0.6028 (ptm) cc_final: 0.5680 (ptm) REVERT: D 89 GLN cc_start: 0.6613 (OUTLIER) cc_final: 0.6255 (pp30) REVERT: D 197 GLU cc_start: 0.8165 (tt0) cc_final: 0.7832 (mt-10) REVERT: D 316 VAL cc_start: 0.7977 (p) cc_final: 0.7684 (t) REVERT: D 323 MET cc_start: 0.6970 (tpp) cc_final: 0.6717 (ttm) REVERT: D 376 MET cc_start: 0.8502 (ttm) cc_final: 0.8126 (ttm) REVERT: D 401 HIS cc_start: 0.8808 (OUTLIER) cc_final: 0.8457 (t-90) REVERT: D 441 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8348 (tptm) outliers start: 73 outliers final: 35 residues processed: 287 average time/residue: 0.5350 time to fit residues: 178.1809 Evaluate side-chains 264 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 215 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 256 THR Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain C residue 22 GLU Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 603 TYR Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 634 GLU Chi-restraints excluded: chain D residue 723 GLU Chi-restraints excluded: chain D residue 750 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 138 optimal weight: 0.0270 chunk 15 optimal weight: 4.9990 chunk 166 optimal weight: 0.0870 chunk 188 optimal weight: 5.9990 chunk 230 optimal weight: 5.9990 chunk 246 optimal weight: 0.0670 chunk 49 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 119 optimal weight: 0.9980 chunk 214 optimal weight: 4.9990 chunk 161 optimal weight: 5.9990 overall best weight: 0.3554 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS B 63 ASN B 117 ASN B 221 GLN D 51 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.212596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.171342 restraints weight = 25164.703| |-----------------------------------------------------------------------------| r_work (start): 0.3909 rms_B_bonded: 2.26 r_work: 0.3579 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.5295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 22703 Z= 0.116 Angle : 0.592 11.262 30950 Z= 0.293 Chirality : 0.041 0.269 3452 Planarity : 0.004 0.056 3876 Dihedral : 4.522 57.599 3450 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.02 % Favored : 96.94 % Rotamer: Outliers : 2.74 % Allowed : 23.65 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 are not related in a simple way. whole: 1.23 (0.16), residues: 2684 helix: 1.47 (0.13), residues: 1728 sheet: 0.01 (0.65), residues: 66 loop : -0.34 (0.21), residues: 890 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 98 TYR 0.024 0.001 TYR A 128 PHE 0.032 0.001 PHE A 529 TRP 0.068 0.001 TRP A 534 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00247 (22668) covalent geometry : angle 0.57908 (30854) SS BOND : bond 0.00625 ( 9) SS BOND : angle 1.38400 ( 18) hydrogen bonds : bond 0.04071 ( 1286) hydrogen bonds : angle 4.46476 ( 3801) link_BETA1-4 : bond 0.00333 ( 12) link_BETA1-4 : angle 1.27028 ( 36) link_NAG-ASN : bond 0.00463 ( 14) link_NAG-ASN : angle 3.05886 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 227 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.6175 (tpp) cc_final: 0.5780 (mmp) REVERT: A 119 MET cc_start: 0.6505 (OUTLIER) cc_final: 0.6178 (ttm) REVERT: A 129 TYR cc_start: 0.7010 (OUTLIER) cc_final: 0.6133 (t80) REVERT: A 193 ILE cc_start: 0.5511 (OUTLIER) cc_final: 0.5241 (pt) REVERT: A 198 LEU cc_start: 0.6509 (OUTLIER) cc_final: 0.6201 (mt) REVERT: A 223 VAL cc_start: 0.6598 (OUTLIER) cc_final: 0.6359 (t) REVERT: A 421 PHE cc_start: 0.6793 (m-80) cc_final: 0.6546 (m-80) REVERT: A 458 LEU cc_start: 0.6428 (OUTLIER) cc_final: 0.6223 (tt) REVERT: B 53 ASN cc_start: 0.5627 (t0) cc_final: 0.5224 (m-40) REVERT: B 152 MET cc_start: 0.9111 (mmm) cc_final: 0.8861 (mmp) REVERT: B 197 GLU cc_start: 0.8215 (tt0) cc_final: 0.7899 (mt-10) REVERT: B 401 HIS cc_start: 0.8864 (OUTLIER) cc_final: 0.8502 (t-90) REVERT: B 441 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8207 (tppp) REVERT: B 560 LEU cc_start: 0.8792 (mt) cc_final: 0.8510 (mt) REVERT: C 83 ILE cc_start: 0.6507 (OUTLIER) cc_final: 0.6174 (mt) REVERT: C 104 TRP cc_start: 0.5701 (m100) cc_final: 0.5422 (m100) REVERT: C 436 MET cc_start: 0.6859 (OUTLIER) cc_final: 0.6140 (ttm) REVERT: C 445 ASP cc_start: 0.4237 (m-30) cc_final: 0.4028 (m-30) REVERT: C 452 LYS cc_start: 0.4769 (OUTLIER) cc_final: 0.4492 (tptt) REVERT: D 45 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7574 (mm) REVERT: D 62 MET cc_start: 0.5958 (ptm) cc_final: 0.5622 (ptm) REVERT: D 81 GLN cc_start: 0.7239 (OUTLIER) cc_final: 0.7022 (mp10) REVERT: D 89 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.6078 (pp30) REVERT: D 197 GLU cc_start: 0.8166 (tt0) cc_final: 0.7853 (mt-10) REVERT: D 316 VAL cc_start: 0.7977 (p) cc_final: 0.7694 (t) REVERT: D 332 MET cc_start: 0.6848 (tpp) cc_final: 0.6344 (tpt) REVERT: D 376 MET cc_start: 0.8528 (ttm) cc_final: 0.8165 (ttm) REVERT: D 401 HIS cc_start: 0.8754 (OUTLIER) cc_final: 0.8411 (t-90) outliers start: 65 outliers final: 35 residues processed: 273 average time/residue: 0.5357 time to fit residues: 169.2118 Evaluate side-chains 259 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 209 time to evaluate : 0.795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain B residue 26 LYS Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 193 ILE Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 603 TYR Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 634 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 20.0000 chunk 112 optimal weight: 3.9990 chunk 200 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 242 optimal weight: 2.9990 chunk 7 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 overall best weight: 1.5684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 117 ASN D 49 ASN D 89 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.209891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.167856 restraints weight = 24803.102| |-----------------------------------------------------------------------------| r_work (start): 0.3871 rms_B_bonded: 2.20 r_work: 0.3527 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22703 Z= 0.153 Angle : 0.656 17.509 30950 Z= 0.325 Chirality : 0.045 0.396 3452 Planarity : 0.004 0.053 3876 Dihedral : 4.821 56.632 3450 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 2.57 % Allowed : 23.82 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 1.16 (0.16), residues: 2684 helix: 1.39 (0.13), residues: 1710 sheet: 0.12 (0.64), residues: 66 loop : -0.27 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 98 TYR 0.023 0.002 TYR A 128 PHE 0.030 0.002 PHE C 570 TRP 0.071 0.002 TRP A 534 HIS 0.005 0.001 HIS D 374 Details of bonding type rmsd covalent geometry : bond 0.00347 (22668) covalent geometry : angle 0.62741 (30854) SS BOND : bond 0.00816 ( 9) SS BOND : angle 1.94514 ( 18) hydrogen bonds : bond 0.04641 ( 1286) hydrogen bonds : angle 4.57121 ( 3801) link_BETA1-4 : bond 0.00396 ( 12) link_BETA1-4 : angle 1.40997 ( 36) link_NAG-ASN : bond 0.00518 ( 14) link_NAG-ASN : angle 5.00514 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5368 Ramachandran restraints generated. 2684 Oldfield, 0 Emsley, 2684 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 234 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.6205 (tpp) cc_final: 0.5784 (mmp) REVERT: A 119 MET cc_start: 0.6490 (OUTLIER) cc_final: 0.6172 (ttm) REVERT: A 129 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.6242 (t80) REVERT: A 193 ILE cc_start: 0.5455 (OUTLIER) cc_final: 0.5249 (pt) REVERT: A 198 LEU cc_start: 0.6559 (OUTLIER) cc_final: 0.6225 (mt) REVERT: A 223 VAL cc_start: 0.6647 (OUTLIER) cc_final: 0.6411 (t) REVERT: A 464 LEU cc_start: 0.6385 (tm) cc_final: 0.6025 (tp) REVERT: A 534 TRP cc_start: 0.5652 (m-90) cc_final: 0.5443 (m-90) REVERT: B 53 ASN cc_start: 0.5725 (t0) cc_final: 0.5304 (m-40) REVERT: B 82 MET cc_start: 0.2743 (pmm) cc_final: 0.2091 (ppp) REVERT: B 152 MET cc_start: 0.9084 (mmm) cc_final: 0.8864 (mmp) REVERT: B 197 GLU cc_start: 0.8278 (tt0) cc_final: 0.7961 (mt-10) REVERT: B 401 HIS cc_start: 0.8972 (OUTLIER) cc_final: 0.8603 (t-90) REVERT: B 441 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8176 (tppp) REVERT: C 83 ILE cc_start: 0.6547 (OUTLIER) cc_final: 0.6201 (mt) REVERT: C 162 TYR cc_start: 0.4117 (m-10) cc_final: 0.3741 (m-10) REVERT: C 436 MET cc_start: 0.6796 (OUTLIER) cc_final: 0.6102 (ttm) REVERT: C 452 LYS cc_start: 0.4810 (OUTLIER) cc_final: 0.4483 (tptt) REVERT: D 62 MET cc_start: 0.5891 (ptm) cc_final: 0.5523 (ptm) REVERT: D 81 GLN cc_start: 0.7291 (OUTLIER) cc_final: 0.6947 (mp10) REVERT: D 89 GLN cc_start: 0.6382 (OUTLIER) cc_final: 0.6119 (pp30) REVERT: D 136 ASP cc_start: 0.7558 (OUTLIER) cc_final: 0.7065 (m-30) REVERT: D 197 GLU cc_start: 0.8274 (tt0) cc_final: 0.7992 (mt-10) REVERT: D 316 VAL cc_start: 0.8061 (p) cc_final: 0.7775 (t) REVERT: D 393 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7045 (mtp180) REVERT: D 401 HIS cc_start: 0.8926 (OUTLIER) cc_final: 0.8568 (t-90) REVERT: D 441 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8404 (tptm) REVERT: D 750 MET cc_start: 0.5175 (OUTLIER) cc_final: 0.4937 (mmm) outliers start: 61 outliers final: 32 residues processed: 278 average time/residue: 0.5352 time to fit residues: 173.1088 Evaluate side-chains 272 residues out of total 2378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 223 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 119 MET Chi-restraints excluded: chain A residue 129 TYR Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 213 ILE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 225 ILE Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 407 ILE Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 585 VAL Chi-restraints excluded: chain B residue 318 VAL Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 401 HIS Chi-restraints excluded: chain B residue 441 LYS Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 581 VAL Chi-restraints excluded: chain B residue 634 GLU Chi-restraints excluded: chain B residue 697 ARG Chi-restraints excluded: chain B residue 750 MET Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 83 ILE Chi-restraints excluded: chain C residue 140 LEU Chi-restraints excluded: chain C residue 361 VAL Chi-restraints excluded: chain C residue 383 CYS Chi-restraints excluded: chain C residue 436 MET Chi-restraints excluded: chain C residue 440 VAL Chi-restraints excluded: chain C residue 452 LYS Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 576 ILE Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 603 TYR Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 89 GLN Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain D residue 257 SER Chi-restraints excluded: chain D residue 339 VAL Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 393 ARG Chi-restraints excluded: chain D residue 401 HIS Chi-restraints excluded: chain D residue 441 LYS Chi-restraints excluded: chain D residue 560 LEU Chi-restraints excluded: chain D residue 581 VAL Chi-restraints excluded: chain D residue 611 SER Chi-restraints excluded: chain D residue 615 ASP Chi-restraints excluded: chain D residue 750 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 266 random chunks: chunk 200 optimal weight: 0.6980 chunk 102 optimal weight: 0.6980 chunk 94 optimal weight: 10.0000 chunk 253 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 250 optimal weight: 2.9990 chunk 262 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 117 ASN D 89 GLN D 373 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.210202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.166493 restraints weight = 24894.259| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 2.24 r_work: 0.3528 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3480 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7562 moved from start: 0.5571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22703 Z= 0.136 Angle : 0.634 17.674 30950 Z= 0.313 Chirality : 0.043 0.322 3452 Planarity : 0.004 0.053 3876 Dihedral : 4.716 57.234 3450 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.98 % Favored : 96.98 % Rotamer: Outliers : 2.44 % Allowed : 23.95 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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 are not related in a simple way. whole: 1.18 (0.16), residues: 2684 helix: 1.41 (0.13), residues: 1716 sheet: 0.12 (0.64), residues: 66 loop : -0.30 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 98 TYR 0.023 0.001 TYR A 128 PHE 0.031 0.001 PHE C 570 TRP 0.068 0.002 TRP A 534 HIS 0.005 0.001 HIS D 373 Details of bonding type rmsd covalent geometry : bond 0.00302 (22668) covalent geometry : angle 0.60793 (30854) SS BOND : bond 0.00755 ( 9) SS BOND : angle 1.67839 ( 18) hydrogen bonds : bond 0.04429 ( 1286) hydrogen bonds : angle 4.53223 ( 3801) link_BETA1-4 : bond 0.00392 ( 12) link_BETA1-4 : angle 1.32137 ( 36) link_NAG-ASN : bond 0.00645 ( 14) link_NAG-ASN : angle 4.64504 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7344.69 seconds wall clock time: 125 minutes 45.36 seconds (7545.36 seconds total)