Starting phenix.real_space_refine on Sun Aug 24 02:02:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd3_36174/08_2025/8jd3_36174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd3_36174/08_2025/8jd3_36174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8jd3_36174/08_2025/8jd3_36174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd3_36174/08_2025/8jd3_36174.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd3_36174/08_2025/8jd3_36174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd3_36174/08_2025/8jd3_36174_neut.cif" } resolution = 3.3 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= 0.031 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 115 5.16 5 Cl 1 4.86 5 C 10099 2.51 5 N 2672 2.21 5 O 2882 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15770 Number of models: 1 Model: "" Number of chains: 8 Chain: "2" Number of atoms: 5793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 774, 5793 Classifications: {'peptide': 774} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 37, 'TRANS': 736} Chain breaks: 1 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 302 Unresolved non-hydrogen dihedrals: 200 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 5, 'ARG:plan': 15, 'GLN:plan1': 5, 'ASN:plan1': 4, 'HIS:plan': 1, 'TRP:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 193 Chain: "3" Number of atoms: 5744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 763, 5744 Classifications: {'peptide': 763} Incomplete info: {'truncation_to_alanine': 78} Link IDs: {'PTRANS': 30, 'TRANS': 732} Chain breaks: 2 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 383 Unresolved non-hydrogen dihedrals: 258 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'ARG:plan': 8, 'HIS:plan': 1, 'TRP:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 184 Chain: "A" Number of atoms: 1491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1491 Classifications: {'peptide': 219} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 72} Link IDs: {'PTRANS': 2, 'TRANS': 216} Chain breaks: 1 Unresolved non-hydrogen bonds: 286 Unresolved non-hydrogen angles: 347 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 11, 'ARG:plan': 6, 'ASP:plan': 11, 'ASN:plan1': 4, 'GLN:plan1': 2, 'TYR:plan': 4, 'HIS:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 166 Chain: "B" Number of atoms: 2220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2220 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 99} Link IDs: {'PTRANS': 5, 'TRANS': 330} Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 467 Unresolved non-hydrogen dihedrals: 289 Unresolved non-hydrogen chiralities: 29 Planarities with less than four sites: {'ASP:plan': 19, 'GLN:plan1': 8, 'ARG:plan': 12, 'ASN:plan1': 9, 'HIS:plan': 2, 'TYR:plan': 2, 'GLU:plan': 4, 'PHE:plan': 3} Unresolved non-hydrogen planarities: 234 Chain: "C" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 347 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 4, 'TRANS': 49} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "2" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 62 Unusual residues: {'CLR': 1, 'HZR': 1} Inner-chain residues flagged as termini: ['pdbres="GLU 2 902 "'] Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1} Link IDs: {None: 2} Chain: "3" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "3" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 103 Unusual residues: {'CLR': 2, 'PEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 3.85, per 1000 atoms: 0.24 Number of scatterers: 15770 At special positions: 0 Unit cell: (111.384, 121.023, 240.975, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 115 16.00 P 1 15.00 O 2882 8.00 N 2672 7.00 C 10099 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS 2 50 " - pdb=" SG CYS 2 92 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 234 " - pdb=" SG CYS 2 518 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 355 " - pdb=" SG CYS 2 362 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 400 " - pdb=" SG CYS 2 407 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 500 " - pdb=" SG CYS 2 519 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 504 " - pdb=" SG CYS 2 522 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 525 " - pdb=" SG CYS 2 537 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 540 " - pdb=" SG CYS 2 553 " distance=2.03 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 57 " - pdb=" SG CYS 3 99 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 240 " - pdb=" SG CYS 3 527 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 361 " - pdb=" SG CYS 3 373 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 412 " - pdb=" SG CYS 3 419 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 509 " - pdb=" SG CYS 3 528 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 513 " - pdb=" SG CYS 3 531 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 534 " - pdb=" SG CYS 3 546 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 549 " - pdb=" SG CYS 3 562 " distance=2.03 Simple disulfide: pdb=" SG CYS 3 641 " - pdb=" SG CYS 3 730 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.59 Conformation dependent library (CDL) restraints added in 781.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 24 sheets defined 42.4% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain '2' and resid 59 through 75 Processing helix chain '2' and resid 94 through 108 removed outlier: 3.550A pdb=" N LEU 2 103 " --> pdb=" O LEU 2 99 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ALA 2 108 " --> pdb=" O ASP 2 104 " (cutoff:3.500A) Processing helix chain '2' and resid 144 through 158 removed outlier: 3.597A pdb=" N GLN 2 150 " --> pdb=" O ASP 2 146 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL 2 151 " --> pdb=" O VAL 2 147 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE 2 158 " --> pdb=" O LEU 2 154 " (cutoff:3.500A) Processing helix chain '2' and resid 169 through 174 removed outlier: 3.592A pdb=" N LEU 2 172 " --> pdb=" O SER 2 169 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N SER 2 173 " --> pdb=" O ALA 2 170 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ASP 2 174 " --> pdb=" O LYS 2 171 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 169 through 174' Processing helix chain '2' and resid 187 through 202 removed outlier: 4.026A pdb=" N GLN 2 191 " --> pdb=" O PRO 2 187 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LYS 2 193 " --> pdb=" O PHE 2 189 " (cutoff:3.500A) Processing helix chain '2' and resid 216 through 231 removed outlier: 3.950A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ARG 2 231 " --> pdb=" O GLU 2 227 " (cutoff:3.500A) Processing helix chain '2' and resid 246 through 260 removed outlier: 4.202A pdb=" N LYS 2 260 " --> pdb=" O ALA 2 256 " (cutoff:3.500A) Processing helix chain '2' and resid 271 through 285 Processing helix chain '2' and resid 324 through 333 removed outlier: 3.664A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 342 through 354 removed outlier: 4.404A pdb=" N ARG 2 346 " --> pdb=" O ASN 2 342 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N GLU 2 347 " --> pdb=" O PRO 2 343 " (cutoff:3.500A) Processing helix chain '2' and resid 356 through 360 Processing helix chain '2' and resid 375 through 377 No H-bonds generated for 'chain '2' and resid 375 through 377' Processing helix chain '2' and resid 378 through 400 removed outlier: 4.093A pdb=" N ALA 2 391 " --> pdb=" O ALA 2 387 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET 2 395 " --> pdb=" O ALA 2 391 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N HIS 2 396 " --> pdb=" O LEU 2 392 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS 2 400 " --> pdb=" O HIS 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 407 through 411 removed outlier: 3.680A pdb=" N ARG 2 411 " --> pdb=" O ASP 2 408 " (cutoff:3.500A) Processing helix chain '2' and resid 414 through 422 removed outlier: 3.693A pdb=" N LEU 2 418 " --> pdb=" O ASN 2 414 " (cutoff:3.500A) Processing helix chain '2' and resid 568 through 592 Processing helix chain '2' and resid 595 through 600 removed outlier: 3.555A pdb=" N LYS 2 599 " --> pdb=" O THR 2 595 " (cutoff:3.500A) Processing helix chain '2' and resid 604 through 624 removed outlier: 4.337A pdb=" N THR 2 620 " --> pdb=" O CYS 2 616 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ILE 2 622 " --> pdb=" O CYS 2 618 " (cutoff:3.500A) Processing helix chain '2' and resid 628 through 663 removed outlier: 3.864A pdb=" N LEU 2 637 " --> pdb=" O THR 2 633 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU 2 639 " --> pdb=" O ARG 2 635 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLY 2 640 " --> pdb=" O ARG 2 636 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE 2 643 " --> pdb=" O LEU 2 639 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS 2 646 " --> pdb=" O ALA 2 642 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS 2 653 " --> pdb=" O ALA 2 649 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N THR 2 654 " --> pdb=" O LEU 2 650 " (cutoff:3.500A) Processing helix chain '2' and resid 677 through 701 removed outlier: 3.547A pdb=" N GLN 2 690 " --> pdb=" O LEU 2 686 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL 2 700 " --> pdb=" O ALA 2 696 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLU 2 701 " --> pdb=" O TRP 2 697 " (cutoff:3.500A) Processing helix chain '2' and resid 724 through 727 Processing helix chain '2' and resid 728 through 747 Processing helix chain '2' and resid 762 through 784 Proline residue: 2 778 - end of helix removed outlier: 3.830A pdb=" N SER 2 784 " --> pdb=" O PHE 2 780 " (cutoff:3.500A) Processing helix chain '2' and resid 788 through 810 Processing helix chain '2' and resid 810 through 819 Processing helix chain '3' and resid 66 through 82 Processing helix chain '3' and resid 101 through 110 removed outlier: 3.576A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) Processing helix chain '3' and resid 150 through 162 Processing helix chain '3' and resid 193 through 208 removed outlier: 4.115A pdb=" N GLN 3 197 " --> pdb=" O PRO 3 193 " (cutoff:3.500A) Processing helix chain '3' and resid 222 through 237 Processing helix chain '3' and resid 257 through 266 removed outlier: 3.511A pdb=" N LYS 3 266 " --> pdb=" O GLU 3 262 " (cutoff:3.500A) Processing helix chain '3' and resid 277 through 292 removed outlier: 3.851A pdb=" N ARG 3 282 " --> pdb=" O SER 3 278 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N GLU 3 283 " --> pdb=" O ASP 3 279 " (cutoff:3.500A) Processing helix chain '3' and resid 330 through 339 removed outlier: 3.555A pdb=" N SER 3 339 " --> pdb=" O ARG 3 335 " (cutoff:3.500A) Processing helix chain '3' and resid 348 through 359 removed outlier: 4.313A pdb=" N ARG 3 352 " --> pdb=" O ASN 3 348 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASP 3 353 " --> pdb=" O PRO 3 349 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N PHE 3 359 " --> pdb=" O TRP 3 355 " (cutoff:3.500A) Processing helix chain '3' and resid 389 through 412 removed outlier: 4.173A pdb=" N MET 3 400 " --> pdb=" O ALA 3 396 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET 3 407 " --> pdb=" O ALA 3 403 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLN 3 408 " --> pdb=" O LEU 3 404 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR 3 410 " --> pdb=" O LYS 3 406 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS 3 412 " --> pdb=" O GLN 3 408 " (cutoff:3.500A) Processing helix chain '3' and resid 419 through 423 Processing helix chain '3' and resid 426 through 433 Processing helix chain '3' and resid 449 through 451 No H-bonds generated for 'chain '3' and resid 449 through 451' Processing helix chain '3' and resid 493 through 497 Processing helix chain '3' and resid 574 through 602 removed outlier: 4.217A pdb=" N GLY 3 579 " --> pdb=" O ALA 3 575 " (cutoff:3.500A) Proline residue: 3 580 - end of helix removed outlier: 3.592A pdb=" N ASN 3 602 " --> pdb=" O PHE 3 598 " (cutoff:3.500A) Processing helix chain '3' and resid 611 through 634 removed outlier: 3.862A pdb=" N THR 3 629 " --> pdb=" O SER 3 625 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE 3 630 " --> pdb=" O TYR 3 626 " (cutoff:3.500A) Processing helix chain '3' and resid 637 through 666 removed outlier: 3.793A pdb=" N GLY 3 649 " --> pdb=" O ARG 3 645 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N PHE 3 652 " --> pdb=" O LEU 3 648 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE 3 666 " --> pdb=" O LYS 3 662 " (cutoff:3.500A) Processing helix chain '3' and resid 685 through 710 removed outlier: 3.656A pdb=" N GLN 3 699 " --> pdb=" O LEU 3 695 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU 3 710 " --> pdb=" O TRP 3 706 " (cutoff:3.500A) Processing helix chain '3' and resid 733 through 759 Processing helix chain '3' and resid 767 through 793 Proline residue: 3 787 - end of helix Processing helix chain '3' and resid 795 through 829 removed outlier: 3.525A pdb=" N MET 3 803 " --> pdb=" O GLN 3 799 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N CYS 3 804 " --> pdb=" O THR 3 800 " (cutoff:3.500A) Proline residue: 3 821 - end of helix Processing helix chain 'A' and resid 9 through 33 removed outlier: 3.622A pdb=" N ASP A 20 " --> pdb=" O SER A 16 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 194 removed outlier: 3.686A pdb=" N ASP A 193 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 removed outlier: 3.929A pdb=" N TRP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 241 through 256 Processing helix chain 'A' and resid 272 through 279 removed outlier: 3.699A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 308 removed outlier: 4.575A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 317 removed outlier: 3.686A pdb=" N ASP A 315 " --> pdb=" O ASN A 311 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N THR A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.570A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 36 removed outlier: 4.706A pdb=" N ALA B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N THR B 29 " --> pdb=" O CYS B 25 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 28 removed outlier: 3.561A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE C 25 " --> pdb=" O MET C 21 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE C 28 " --> pdb=" O ASN C 24 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 41 removed outlier: 3.793A pdb=" N ASP C 36 " --> pdb=" O LYS C 32 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N CYS C 41 " --> pdb=" O LEU C 37 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 52 Processing sheet with id=AA1, first strand: chain '2' and resid 84 through 90 removed outlier: 7.038A pdb=" N LEU 2 32 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N HIS 2 87 " --> pdb=" O LEU 2 32 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU 2 34 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N LEU 2 89 " --> pdb=" O LEU 2 34 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N GLY 2 36 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N VAL 2 33 " --> pdb=" O ILE 2 136 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLY 2 138 " --> pdb=" O VAL 2 33 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU 2 37 " --> pdb=" O ILE 2 140 " (cutoff:3.500A) removed outlier: 8.319A pdb=" N ILE 2 163 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL 2 139 " --> pdb=" O ILE 2 163 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '2' and resid 234 through 241 removed outlier: 7.680A pdb=" N VAL 2 207 " --> pdb=" O ALA 2 236 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N SER 2 238 " --> pdb=" O VAL 2 207 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N THR 2 209 " --> pdb=" O SER 2 238 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS 2 240 " --> pdb=" O THR 2 209 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ALA 2 211 " --> pdb=" O LYS 2 240 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL 2 265 " --> pdb=" O TYR 2 206 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER 2 208 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '2' and resid 315 through 319 removed outlier: 4.074A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain '2' and resid 427 through 428 removed outlier: 3.673A pdb=" N PHE 2 428 " --> pdb=" O VAL 2 441 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VAL 2 441 " --> pdb=" O PHE 2 428 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain '2' and resid 509 through 510 Processing sheet with id=AA6, first strand: chain '2' and resid 545 through 548 removed outlier: 6.591A pdb=" N PHE 2 554 " --> pdb=" O PRO 2 546 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '2' and resid 706 through 710 removed outlier: 3.562A pdb=" N THR 2 718 " --> pdb=" O GLU 2 708 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N ALA 2 710 " --> pdb=" O VAL 2 716 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N VAL 2 716 " --> pdb=" O ALA 2 710 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '3' and resid 91 through 97 removed outlier: 3.872A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N GLY 3 43 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N VAL 3 40 " --> pdb=" O GLY 3 144 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ILE 3 146 " --> pdb=" O VAL 3 40 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLY 3 42 " --> pdb=" O ILE 3 146 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N ILE 3 169 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N VAL 3 145 " --> pdb=" O ILE 3 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '3' and resid 48 through 50 removed outlier: 4.820A pdb=" N ARG 3 59 " --> pdb=" O GLU 3 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '3' and resid 240 through 247 removed outlier: 7.524A pdb=" N VAL 3 213 " --> pdb=" O ALA 3 242 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ALA 3 244 " --> pdb=" O VAL 3 213 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N THR 3 215 " --> pdb=" O ALA 3 244 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS 3 246 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ALA 3 217 " --> pdb=" O LYS 3 246 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N VAL 3 271 " --> pdb=" O TYR 3 212 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N VAL 3 272 " --> pdb=" O VAL 3 298 " (cutoff:3.500A) removed outlier: 5.866A pdb=" N TRP 3 297 " --> pdb=" O ILE 3 321 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N LEU 3 323 " --> pdb=" O TRP 3 297 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ALA 3 299 " --> pdb=" O LEU 3 323 " (cutoff:3.500A) removed outlier: 9.509A pdb=" N LEU 3 325 " --> pdb=" O ALA 3 299 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA 3 320 " --> pdb=" O PHE 3 471 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR 3 466 " --> pdb=" O HIS 3 485 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N HIS 3 485 " --> pdb=" O TYR 3 466 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL 3 468 " --> pdb=" O VAL 3 483 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '3' and resid 439 through 441 Processing sheet with id=AB3, first strand: chain '3' and resid 518 through 521 Processing sheet with id=AB4, first strand: chain '3' and resid 538 through 542 removed outlier: 3.748A pdb=" N ALA 3 541 " --> pdb=" O THR 3 545 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N THR 3 545 " --> pdb=" O ALA 3 541 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain '3' and resid 553 through 554 Processing sheet with id=AB6, first strand: chain '3' and resid 714 through 717 removed outlier: 4.249A pdb=" N ARG 3 715 " --> pdb=" O LYS 3 729 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N LYS 3 729 " --> pdb=" O ARG 3 715 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR 3 717 " --> pdb=" O ILE 3 727 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE 3 727 " --> pdb=" O TYR 3 717 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.505A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 7.098A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 186 through 189 Processing sheet with id=AB9, first strand: chain 'B' and resid 50 through 51 removed outlier: 4.441A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 70 through 73 Processing sheet with id=AC2, first strand: chain 'B' and resid 100 through 103 removed outlier: 3.590A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 149 through 151 removed outlier: 7.476A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 198 through 201 removed outlier: 4.127A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.297A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 240 through 241 removed outlier: 3.933A pdb=" N PHE B 253 " --> pdb=" O PHE B 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 273 through 278 removed outlier: 4.543A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA B 287 " --> pdb=" O ASN B 295 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N ASN B 295 " --> pdb=" O ALA B 287 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) 687 hydrogen bonds defined for protein. 1992 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: 3.03 Time building geometry restraints manager: 2.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2554 1.31 - 1.44: 4366 1.44 - 1.56: 9037 1.56 - 1.69: 12 1.69 - 1.81: 150 Bond restraints: 16119 Sorted by residual: bond pdb=" C18 HZR 2 901 " pdb=" C19 HZR 2 901 " ideal model delta sigma weight residual 1.353 1.525 -0.172 2.00e-02 2.50e+03 7.41e+01 bond pdb=" C19 HZR 2 901 " pdb=" N20 HZR 2 901 " ideal model delta sigma weight residual 1.353 1.484 -0.131 2.00e-02 2.50e+03 4.30e+01 bond pdb=" C10 PEF 3 904 " pdb=" O2 PEF 3 904 " ideal model delta sigma weight residual 1.330 1.453 -0.123 2.00e-02 2.50e+03 3.78e+01 bond pdb=" C03 HZR 2 901 " pdb=" C05 HZR 2 901 " ideal model delta sigma weight residual 1.377 1.496 -0.119 2.00e-02 2.50e+03 3.56e+01 bond pdb=" C02 HZR 2 901 " pdb=" N20 HZR 2 901 " ideal model delta sigma weight residual 1.388 1.485 -0.097 2.00e-02 2.50e+03 2.35e+01 ... (remaining 16114 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.12: 21901 3.12 - 6.25: 86 6.25 - 9.37: 7 9.37 - 12.50: 2 12.50 - 15.62: 1 Bond angle restraints: 21997 Sorted by residual: angle pdb=" O3P PEF 3 904 " pdb=" P PEF 3 904 " pdb=" O4P PEF 3 904 " ideal model delta sigma weight residual 93.96 109.58 -15.62 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C05 HZR 2 901 " pdb=" N06 HZR 2 901 " pdb=" C17 HZR 2 901 " ideal model delta sigma weight residual 115.44 125.48 -10.04 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O1P PEF 3 904 " pdb=" P PEF 3 904 " pdb=" O2P PEF 3 904 " ideal model delta sigma weight residual 119.53 109.94 9.59 3.00e+00 1.11e-01 1.02e+01 angle pdb=" CB MET 3 803 " pdb=" CG MET 3 803 " pdb=" SD MET 3 803 " ideal model delta sigma weight residual 112.70 121.74 -9.04 3.00e+00 1.11e-01 9.09e+00 angle pdb=" C31 PEF 3 904 " pdb=" C30 PEF 3 904 " pdb=" O3 PEF 3 904 " ideal model delta sigma weight residual 111.02 120.05 -9.03 3.00e+00 1.11e-01 9.05e+00 ... (remaining 21992 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 8890 17.95 - 35.90: 615 35.90 - 53.85: 133 53.85 - 71.80: 31 71.80 - 89.75: 16 Dihedral angle restraints: 9685 sinusoidal: 3455 harmonic: 6230 Sorted by residual: dihedral pdb=" CB CYS 2 504 " pdb=" SG CYS 2 504 " pdb=" SG CYS 2 522 " pdb=" CB CYS 2 522 " ideal model delta sinusoidal sigma weight residual -86.00 -174.70 88.70 1 1.00e+01 1.00e-02 9.38e+01 dihedral pdb=" CB CYS 2 400 " pdb=" SG CYS 2 400 " pdb=" SG CYS 2 407 " pdb=" CB CYS 2 407 " ideal model delta sinusoidal sigma weight residual 93.00 178.23 -85.23 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS 3 57 " pdb=" SG CYS 3 57 " pdb=" SG CYS 3 99 " pdb=" CB CYS 3 99 " ideal model delta sinusoidal sigma weight residual 93.00 11.99 81.01 1 1.00e+01 1.00e-02 8.10e+01 ... (remaining 9682 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.966: 2571 0.966 - 1.932: 0 1.932 - 2.897: 0 2.897 - 3.863: 0 3.863 - 4.829: 1 Chirality restraints: 2572 Sorted by residual: chirality pdb=" C09 HZR 2 901 " pdb=" C08 HZR 2 901 " pdb=" C10 HZR 2 901 " pdb=" C16 HZR 2 901 " both_signs ideal model delta sigma weight residual False 2.48 -2.35 4.83 2.00e-01 2.50e+01 5.83e+02 chirality pdb=" C2 PEF 3 904 " pdb=" C1 PEF 3 904 " pdb=" C3 PEF 3 904 " pdb=" O2 PEF 3 904 " both_signs ideal model delta sigma weight residual False -2.35 -2.58 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CB ILE B 123 " pdb=" CA ILE B 123 " pdb=" CG1 ILE B 123 " pdb=" CG2 ILE B 123 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 2569 not shown) Planarity restraints: 2800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU B 12 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" CD GLU B 12 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU B 12 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU B 12 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN 3 445 " -0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO 3 446 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO 3 446 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO 3 446 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS 3 761 " -0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO 3 762 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO 3 762 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO 3 762 " -0.018 5.00e-02 4.00e+02 ... (remaining 2797 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1559 2.75 - 3.29: 15466 3.29 - 3.82: 25814 3.82 - 4.36: 28763 4.36 - 4.90: 50559 Nonbonded interactions: 122161 Sorted by model distance: nonbonded pdb=" O LEU B 168 " pdb=" OG1 THR B 177 " model vdw 2.210 3.040 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.256 3.040 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.258 3.040 nonbonded pdb=" O GLN B 9 " pdb=" NE2 GLN B 13 " model vdw 2.283 3.120 nonbonded pdb=" O LYS A 209 " pdb=" ND1 HIS A 213 " model vdw 2.284 3.120 ... (remaining 122156 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 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: 0.020 Extract box with map and model: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.620 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.172 16137 Z= 0.199 Angle : 0.534 15.624 22033 Z= 0.260 Chirality : 0.103 4.829 2572 Planarity : 0.003 0.038 2800 Dihedral : 13.401 89.748 5601 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.13 % Allowed : 0.13 % Favored : 99.73 % 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 aren not related in a simple way. whole: -0.23 (0.18), residues: 2128 helix: 1.43 (0.19), residues: 810 sheet: -0.72 (0.31), residues: 290 loop : -1.30 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG 3 335 TYR 0.015 0.001 TYR 3 656 PHE 0.021 0.001 PHE 2 747 TRP 0.008 0.001 TRP 2 545 HIS 0.002 0.000 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00407 (16119) covalent geometry : angle 0.53395 (21997) SS BOND : bond 0.00147 ( 18) SS BOND : angle 0.73889 ( 36) hydrogen bonds : bond 0.15783 ( 687) hydrogen bonds : angle 5.85807 ( 1992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 264 time to evaluate : 0.644 Fit side-chains revert: symmetry clash REVERT: 2 205 THR cc_start: 0.7741 (m) cc_final: 0.7537 (m) REVERT: B 133 VAL cc_start: 0.5322 (p) cc_final: 0.4933 (m) REVERT: B 200 VAL cc_start: 0.4366 (t) cc_final: 0.4030 (t) outliers start: 2 outliers final: 1 residues processed: 265 average time/residue: 0.1232 time to fit residues: 49.7767 Evaluate side-chains 228 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 902 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 98 optimal weight: 0.8980 chunk 194 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 30.0000 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0040 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 592 HIS ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 338 GLN 3 470 ASN B 16 ASN B 44 GLN B 230 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.234256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.219720 restraints weight = 18129.402| |-----------------------------------------------------------------------------| r_work (start): 0.4432 rms_B_bonded: 0.83 r_work: 0.4108 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.3981 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.1556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16137 Z= 0.151 Angle : 0.551 7.392 22033 Z= 0.282 Chirality : 0.042 0.155 2572 Planarity : 0.003 0.037 2800 Dihedral : 6.956 86.530 2560 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 1.00 % Allowed : 8.27 % Favored : 90.73 % 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 aren not related in a simple way. whole: -0.10 (0.18), residues: 2128 helix: 1.58 (0.18), residues: 817 sheet: -0.57 (0.31), residues: 281 loop : -1.31 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 22 TYR 0.018 0.001 TYR 2 781 PHE 0.017 0.001 PHE 2 67 TRP 0.014 0.001 TRP 2 773 HIS 0.004 0.001 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00352 (16119) covalent geometry : angle 0.55030 (21997) SS BOND : bond 0.00201 ( 18) SS BOND : angle 0.81977 ( 36) hydrogen bonds : bond 0.03953 ( 687) hydrogen bonds : angle 4.11711 ( 1992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 265 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 410 MET cc_start: 0.5591 (tpp) cc_final: 0.5381 (tpp) REVERT: 2 794 MET cc_start: 0.8311 (tpp) cc_final: 0.7987 (mmm) outliers start: 15 outliers final: 10 residues processed: 271 average time/residue: 0.1272 time to fit residues: 52.2588 Evaluate side-chains 244 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 234 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 49 ASP Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 205 optimal weight: 10.0000 chunk 157 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 181 optimal weight: 9.9990 chunk 199 optimal weight: 30.0000 chunk 65 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 197 optimal weight: 20.0000 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 655 ASN 3 408 GLN 3 472 GLN A 346 ASN B 13 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.230048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.207197 restraints weight = 18333.497| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 1.22 r_work: 0.4098 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.4062 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.4062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6903 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16137 Z= 0.214 Angle : 0.599 9.465 22033 Z= 0.310 Chirality : 0.044 0.166 2572 Planarity : 0.004 0.058 2800 Dihedral : 7.082 76.698 2557 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.67 % Allowed : 13.07 % 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 aren not related in a simple way. whole: -0.33 (0.18), residues: 2128 helix: 1.30 (0.18), residues: 813 sheet: -0.66 (0.31), residues: 270 loop : -1.36 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG 2 57 TYR 0.029 0.002 TYR 3 776 PHE 0.022 0.002 PHE 2 67 TRP 0.016 0.001 TRP 3 303 HIS 0.006 0.001 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00516 (16119) covalent geometry : angle 0.59699 (21997) SS BOND : bond 0.00281 ( 18) SS BOND : angle 1.24510 ( 36) hydrogen bonds : bond 0.04439 ( 687) hydrogen bonds : angle 4.20152 ( 1992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 245 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 146 ASP cc_start: 0.7403 (OUTLIER) cc_final: 0.7158 (p0) REVERT: 2 365 HIS cc_start: 0.6534 (OUTLIER) cc_final: 0.6308 (m90) REVERT: 2 794 MET cc_start: 0.8259 (tpp) cc_final: 0.7934 (tpp) outliers start: 25 outliers final: 15 residues processed: 261 average time/residue: 0.1270 time to fit residues: 50.1973 Evaluate side-chains 251 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 234 time to evaluate : 0.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 146 ASP Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 237 THR Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 737 LEU Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 171 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 202 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 142 optimal weight: 0.0010 chunk 167 optimal weight: 0.0370 overall best weight: 0.6666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 13 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.232044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.216708 restraints weight = 18282.180| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 0.87 r_work: 0.4246 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4214 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6644 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16137 Z= 0.137 Angle : 0.535 8.789 22033 Z= 0.276 Chirality : 0.042 0.361 2572 Planarity : 0.004 0.045 2800 Dihedral : 6.564 62.004 2557 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 1.93 % Allowed : 14.73 % Favored : 83.33 % 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 aren not related in a simple way. whole: -0.24 (0.18), residues: 2128 helix: 1.40 (0.18), residues: 819 sheet: -0.73 (0.31), residues: 277 loop : -1.31 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 52 TYR 0.019 0.001 TYR 2 781 PHE 0.015 0.001 PHE 2 269 TRP 0.013 0.001 TRP 2 773 HIS 0.004 0.000 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00319 (16119) covalent geometry : angle 0.53354 (21997) SS BOND : bond 0.00318 ( 18) SS BOND : angle 1.06123 ( 36) hydrogen bonds : bond 0.03699 ( 687) hydrogen bonds : angle 3.98438 ( 1992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: 2 794 MET cc_start: 0.8199 (tpp) cc_final: 0.7825 (mmm) REVERT: 3 285 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7216 (tp) outliers start: 29 outliers final: 22 residues processed: 256 average time/residue: 0.1349 time to fit residues: 51.5602 Evaluate side-chains 253 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 230 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 237 THR Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 774 LEU Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 632 PHE Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 148 optimal weight: 2.9990 chunk 166 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 153 optimal weight: 8.9990 chunk 132 optimal weight: 8.9990 chunk 55 optimal weight: 0.0980 chunk 185 optimal weight: 5.9990 chunk 145 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 193 optimal weight: 30.0000 chunk 138 optimal weight: 0.0980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 593 ASN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN B 119 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.229985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.214326 restraints weight = 18184.835| |-----------------------------------------------------------------------------| r_work (start): 0.4376 rms_B_bonded: 0.87 r_work: 0.4223 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4192 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16137 Z= 0.173 Angle : 0.556 8.952 22033 Z= 0.286 Chirality : 0.043 0.281 2572 Planarity : 0.004 0.047 2800 Dihedral : 6.423 59.955 2557 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.13 % Allowed : 16.07 % Favored : 81.80 % 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 aren not related in a simple way. whole: -0.28 (0.18), residues: 2128 helix: 1.36 (0.18), residues: 819 sheet: -0.82 (0.30), residues: 283 loop : -1.30 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.013 0.001 TYR 2 419 PHE 0.018 0.001 PHE 2 67 TRP 0.013 0.001 TRP 2 773 HIS 0.003 0.000 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00414 (16119) covalent geometry : angle 0.55486 (21997) SS BOND : bond 0.00230 ( 18) SS BOND : angle 1.02348 ( 36) hydrogen bonds : bond 0.03934 ( 687) hydrogen bonds : angle 4.05949 ( 1992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 238 time to evaluate : 0.597 Fit side-chains revert: symmetry clash REVERT: 3 285 ILE cc_start: 0.7735 (OUTLIER) cc_final: 0.7280 (tp) REVERT: B 79 LEU cc_start: 0.6332 (pp) cc_final: 0.5981 (pp) REVERT: B 133 VAL cc_start: 0.5810 (OUTLIER) cc_final: 0.5235 (m) outliers start: 32 outliers final: 24 residues processed: 256 average time/residue: 0.1331 time to fit residues: 51.0817 Evaluate side-chains 257 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 231 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 237 THR Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 632 PHE Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 79 optimal weight: 0.0000 chunk 127 optimal weight: 6.9990 chunk 192 optimal weight: 20.0000 chunk 204 optimal weight: 30.0000 chunk 141 optimal weight: 7.9990 chunk 182 optimal weight: 2.9990 chunk 140 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 187 optimal weight: 6.9990 chunk 202 optimal weight: 20.0000 chunk 157 optimal weight: 20.0000 overall best weight: 3.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 286 ASN 2 592 HIS ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 386 GLN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS B 13 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.221307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.205235 restraints weight = 18066.731| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 0.90 r_work: 0.4143 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.4107 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.4107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.123 16137 Z= 0.494 Angle : 0.841 13.223 22033 Z= 0.439 Chirality : 0.054 0.261 2572 Planarity : 0.006 0.068 2800 Dihedral : 6.954 68.054 2557 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 3.40 % Allowed : 16.87 % Favored : 79.73 % 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 aren not related in a simple way. whole: -1.00 (0.18), residues: 2128 helix: 0.55 (0.18), residues: 819 sheet: -1.19 (0.30), residues: 282 loop : -1.50 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG 2 433 TYR 0.033 0.003 TYR 2 458 PHE 0.034 0.003 PHE 2 67 TRP 0.021 0.003 TRP 2 297 HIS 0.006 0.001 HIS 2 87 Details of bonding type rmsd covalent geometry : bond 0.01196 (16119) covalent geometry : angle 0.83938 (21997) SS BOND : bond 0.00560 ( 18) SS BOND : angle 1.57564 ( 36) hydrogen bonds : bond 0.05924 ( 687) hydrogen bonds : angle 4.87656 ( 1992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 245 time to evaluate : 0.634 Fit side-chains REVERT: 3 183 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8195 (mtp85) REVERT: 3 285 ILE cc_start: 0.7833 (OUTLIER) cc_final: 0.7368 (tp) REVERT: B 79 LEU cc_start: 0.6551 (pp) cc_final: 0.6171 (pp) REVERT: B 133 VAL cc_start: 0.5948 (OUTLIER) cc_final: 0.5495 (m) REVERT: B 333 ASP cc_start: 0.5157 (p0) cc_final: 0.4909 (p0) outliers start: 51 outliers final: 36 residues processed: 273 average time/residue: 0.1326 time to fit residues: 54.3011 Evaluate side-chains 267 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 228 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 237 THR Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 356 SER Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 737 LEU Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 2 residue 814 LEU Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 782 TRP Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 286 LEU Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 93 optimal weight: 0.6980 chunk 167 optimal weight: 10.0000 chunk 138 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 136 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 131 optimal weight: 0.8980 chunk 204 optimal weight: 20.0000 chunk 208 optimal weight: 30.0000 chunk 104 optimal weight: 0.0980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS 3 386 GLN ** 3 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.228341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.212375 restraints weight = 17805.170| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 0.85 r_work: 0.4128 rms_B_bonded: 1.20 restraints_weight: 0.5000 r_work: 0.4063 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work: 0.3963 rms_B_bonded: 4.25 restraints_weight: 0.1250 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7032 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16137 Z= 0.141 Angle : 0.582 9.198 22033 Z= 0.299 Chirality : 0.042 0.192 2572 Planarity : 0.004 0.053 2800 Dihedral : 6.146 59.779 2557 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.67 % Allowed : 17.80 % Favored : 79.53 % 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 aren not related in a simple way. whole: -0.62 (0.18), residues: 2128 helix: 1.08 (0.18), residues: 806 sheet: -1.13 (0.30), residues: 279 loop : -1.41 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 68 TYR 0.023 0.001 TYR 2 781 PHE 0.017 0.001 PHE 2 269 TRP 0.017 0.001 TRP 2 773 HIS 0.006 0.001 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00324 (16119) covalent geometry : angle 0.58128 (21997) SS BOND : bond 0.00252 ( 18) SS BOND : angle 0.86549 ( 36) hydrogen bonds : bond 0.03933 ( 687) hydrogen bonds : angle 4.24473 ( 1992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 235 time to evaluate : 0.624 Fit side-chains REVERT: 2 184 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8627 (m) REVERT: B 16 ASN cc_start: 0.5810 (p0) cc_final: 0.5459 (p0) REVERT: B 79 LEU cc_start: 0.6851 (pp) cc_final: 0.6457 (pp) REVERT: B 133 VAL cc_start: 0.5958 (OUTLIER) cc_final: 0.5307 (m) REVERT: B 333 ASP cc_start: 0.5458 (p0) cc_final: 0.4991 (p0) REVERT: C 21 MET cc_start: 0.4569 (ppp) cc_final: 0.3333 (ppp) outliers start: 40 outliers final: 27 residues processed: 260 average time/residue: 0.1306 time to fit residues: 51.0477 Evaluate side-chains 257 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 237 THR Chi-restraints excluded: chain 2 residue 356 SER Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 623 PHE Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 2 residue 815 HIS Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 786 LEU Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 274 THR Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 127 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 161 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 159 optimal weight: 9.9990 chunk 193 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 179 optimal weight: 9.9990 chunk 50 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 592 HIS 2 655 ASN 3 699 GLN A 346 ASN B 13 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.228598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.213026 restraints weight = 18222.031| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 0.89 r_work: 0.4213 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.4177 rms_B_bonded: 2.23 restraints_weight: 0.2500 r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16137 Z= 0.151 Angle : 0.577 10.233 22033 Z= 0.295 Chirality : 0.042 0.167 2572 Planarity : 0.004 0.053 2800 Dihedral : 5.900 57.641 2557 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 2.47 % Allowed : 18.40 % Favored : 79.13 % 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 aren not related in a simple way. whole: -0.49 (0.18), residues: 2128 helix: 1.22 (0.18), residues: 813 sheet: -1.06 (0.30), residues: 283 loop : -1.40 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 19 TYR 0.021 0.001 TYR 2 745 PHE 0.020 0.001 PHE 2 269 TRP 0.017 0.001 TRP 2 773 HIS 0.005 0.001 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00356 (16119) covalent geometry : angle 0.57659 (21997) SS BOND : bond 0.00234 ( 18) SS BOND : angle 0.73660 ( 36) hydrogen bonds : bond 0.03882 ( 687) hydrogen bonds : angle 4.17336 ( 1992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.671 Fit side-chains REVERT: 2 184 THR cc_start: 0.9058 (OUTLIER) cc_final: 0.8615 (m) REVERT: B 61 MET cc_start: 0.6359 (ppp) cc_final: 0.5942 (ppp) REVERT: B 79 LEU cc_start: 0.6087 (pp) cc_final: 0.5764 (pp) REVERT: B 133 VAL cc_start: 0.5768 (OUTLIER) cc_final: 0.5324 (m) REVERT: B 333 ASP cc_start: 0.4811 (p0) cc_final: 0.4430 (p0) REVERT: C 21 MET cc_start: 0.3886 (ppp) cc_final: 0.2806 (ppp) outliers start: 37 outliers final: 31 residues processed: 262 average time/residue: 0.1293 time to fit residues: 51.2543 Evaluate side-chains 266 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 233 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 237 THR Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 623 PHE Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 783 LEU Chi-restraints excluded: chain 3 residue 786 LEU Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 75 GLN Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 0.1980 chunk 140 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 199 optimal weight: 0.0870 chunk 114 optimal weight: 6.9990 chunk 166 optimal weight: 0.9990 overall best weight: 0.4160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 592 HIS A 22 ASN ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 13 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.230630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.215034 restraints weight = 18173.331| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 0.90 r_work: 0.4127 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.4087 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16137 Z= 0.118 Angle : 0.557 9.287 22033 Z= 0.284 Chirality : 0.041 0.140 2572 Planarity : 0.004 0.049 2800 Dihedral : 5.683 58.144 2557 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.67 % Allowed : 18.67 % Favored : 78.67 % 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 aren not related in a simple way. whole: -0.31 (0.18), residues: 2128 helix: 1.39 (0.18), residues: 818 sheet: -0.87 (0.30), residues: 279 loop : -1.36 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 22 TYR 0.040 0.001 TYR 3 776 PHE 0.017 0.001 PHE 2 584 TRP 0.015 0.001 TRP 2 773 HIS 0.005 0.000 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00269 (16119) covalent geometry : angle 0.55652 (21997) SS BOND : bond 0.00179 ( 18) SS BOND : angle 0.62064 ( 36) hydrogen bonds : bond 0.03601 ( 687) hydrogen bonds : angle 4.05179 ( 1992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 239 time to evaluate : 0.606 Fit side-chains REVERT: 2 184 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8522 (m) REVERT: 3 285 ILE cc_start: 0.7630 (OUTLIER) cc_final: 0.7264 (tp) REVERT: 3 422 MET cc_start: 0.6876 (OUTLIER) cc_final: 0.6526 (ttt) REVERT: B 61 MET cc_start: 0.6549 (ppp) cc_final: 0.6280 (ppp) REVERT: B 68 ARG cc_start: 0.2358 (tmt170) cc_final: 0.2138 (ttt90) REVERT: B 79 LEU cc_start: 0.6534 (pp) cc_final: 0.6180 (pp) REVERT: B 133 VAL cc_start: 0.5855 (OUTLIER) cc_final: 0.5422 (m) REVERT: B 333 ASP cc_start: 0.5389 (p0) cc_final: 0.4884 (p0) REVERT: C 21 MET cc_start: 0.4313 (ppp) cc_final: 0.3218 (ppp) outliers start: 40 outliers final: 31 residues processed: 262 average time/residue: 0.1198 time to fit residues: 47.5620 Evaluate side-chains 270 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 235 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 237 THR Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 623 PHE Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 2 residue 815 HIS Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 619 LEU Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 786 LEU Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 24 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 182 optimal weight: 0.0470 chunk 154 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 118 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 114 optimal weight: 0.6980 chunk 164 optimal weight: 3.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.229796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.214172 restraints weight = 18152.017| |-----------------------------------------------------------------------------| r_work (start): 0.4375 rms_B_bonded: 0.89 r_work: 0.4226 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.4193 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6680 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16137 Z= 0.135 Angle : 0.570 9.495 22033 Z= 0.291 Chirality : 0.042 0.145 2572 Planarity : 0.004 0.048 2800 Dihedral : 5.640 59.653 2557 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.47 % Allowed : 18.67 % Favored : 78.87 % 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 aren not related in a simple way. whole: -0.26 (0.18), residues: 2128 helix: 1.44 (0.18), residues: 817 sheet: -0.84 (0.30), residues: 289 loop : -1.34 (0.19), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 42 TYR 0.019 0.001 TYR 2 745 PHE 0.020 0.001 PHE 2 269 TRP 0.016 0.001 TRP 2 773 HIS 0.005 0.000 HIS 3 346 Details of bonding type rmsd covalent geometry : bond 0.00315 (16119) covalent geometry : angle 0.56989 (21997) SS BOND : bond 0.00194 ( 18) SS BOND : angle 0.64191 ( 36) hydrogen bonds : bond 0.03697 ( 687) hydrogen bonds : angle 4.04101 ( 1992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4256 Ramachandran restraints generated. 2128 Oldfield, 0 Emsley, 2128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 235 time to evaluate : 0.631 Fit side-chains REVERT: 2 168 THR cc_start: 0.8742 (m) cc_final: 0.8378 (m) REVERT: 2 184 THR cc_start: 0.9008 (OUTLIER) cc_final: 0.8481 (m) REVERT: 3 285 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7325 (tp) REVERT: 3 422 MET cc_start: 0.6813 (OUTLIER) cc_final: 0.6487 (ttt) REVERT: B 61 MET cc_start: 0.6114 (ppp) cc_final: 0.5769 (ppp) REVERT: B 68 ARG cc_start: 0.2520 (tmt170) cc_final: 0.2280 (ttt90) REVERT: B 79 LEU cc_start: 0.6073 (pp) cc_final: 0.5758 (pp) REVERT: B 133 VAL cc_start: 0.5787 (OUTLIER) cc_final: 0.5371 (m) REVERT: B 333 ASP cc_start: 0.4860 (p0) cc_final: 0.4560 (p0) REVERT: C 21 MET cc_start: 0.3721 (ppp) cc_final: 0.2795 (ppp) outliers start: 37 outliers final: 31 residues processed: 257 average time/residue: 0.1152 time to fit residues: 44.6472 Evaluate side-chains 266 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 231 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 237 THR Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 623 PHE Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 771 ILE Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 2 residue 815 HIS Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 619 LEU Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 786 LEU Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 133 optimal weight: 0.6980 chunk 111 optimal weight: 0.0770 chunk 74 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 169 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 143 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 153 optimal weight: 5.9990 chunk 100 optimal weight: 0.8980 chunk 128 optimal weight: 10.0000 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.230716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.215267 restraints weight = 18060.650| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 0.87 r_work: 0.4229 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.4196 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.4196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6677 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16137 Z= 0.128 Angle : 0.567 10.480 22033 Z= 0.289 Chirality : 0.041 0.137 2572 Planarity : 0.004 0.048 2800 Dihedral : 5.574 58.953 2557 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.40 % Allowed : 18.93 % Favored : 78.67 % 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 aren not related in a simple way. whole: -0.23 (0.18), residues: 2128 helix: 1.49 (0.18), residues: 811 sheet: -0.84 (0.29), residues: 289 loop : -1.31 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 22 TYR 0.041 0.001 TYR 3 776 PHE 0.039 0.001 PHE 3 652 TRP 0.019 0.001 TRP 3 782 HIS 0.016 0.001 HIS A 188 Details of bonding type rmsd covalent geometry : bond 0.00297 (16119) covalent geometry : angle 0.56706 (21997) SS BOND : bond 0.00176 ( 18) SS BOND : angle 0.61094 ( 36) hydrogen bonds : bond 0.03646 ( 687) hydrogen bonds : angle 4.00685 ( 1992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4052.78 seconds wall clock time: 70 minutes 16.17 seconds (4216.17 seconds total)