Starting phenix.real_space_refine on Sat Jun 14 13:51:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jd3_36174/06_2025/8jd3_36174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jd3_36174/06_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_36174/06_2025/8jd3_36174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jd3_36174/06_2025/8jd3_36174.map" model { file = "/net/cci-nas-00/data/ceres_data/8jd3_36174/06_2025/8jd3_36174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jd3_36174/06_2025/8jd3_36174_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 5, 'ASP:plan': 5, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 15} 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: {'ASP:plan': 9, 'TYR:plan': 4, 'ASN:plan1': 9, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 8} 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: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 11, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} 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: {'GLN:plan1': 8, 'ASP:plan': 19, 'TYR:plan': 2, 'ASN:plan1': 9, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 4, 'ARG:plan': 12} 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, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 3, 'ARG:plan': 2} 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: 10.02, per 1000 atoms: 0.64 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: 3.81 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 1.81 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: 5.21 Time building geometry restraints manager: 4.51 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: 3.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.600 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 36.840 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.520 ------------------------------------------------------------------------------- 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 : 6.60 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (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 TRP 0.008 0.001 TRP 2 545 HIS 0.002 0.000 HIS A 213 PHE 0.021 0.001 PHE 2 747 TYR 0.015 0.001 TYR 3 656 ARG 0.004 0.000 ARG 3 335 Details of bonding type rmsd hydrogen bonds : bond 0.15783 ( 687) hydrogen bonds : angle 5.85807 ( 1992) SS BOND : bond 0.00147 ( 18) SS BOND : angle 0.73889 ( 36) covalent geometry : bond 0.00407 (16119) covalent geometry : angle 0.53395 (21997) *********************** 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 : 1.551 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: 0.2515 time to fit residues: 101.5884 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 : 1.747 ------------------------------------------------------------------------------- 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 179 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 166 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 123 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 374 GLN 2 592 HIS ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 197 GLN 3 338 GLN 3 470 ASN B 16 ASN B 44 GLN B 230 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.232028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.217339 restraints weight = 18041.727| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 0.83 r_work: 0.4063 rms_B_bonded: 1.24 restraints_weight: 0.5000 r_work: 0.3842 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7216 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16137 Z= 0.185 Angle : 0.583 7.489 22033 Z= 0.300 Chirality : 0.043 0.152 2572 Planarity : 0.004 0.039 2800 Dihedral : 7.076 85.643 2560 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 1.00 % Allowed : 9.07 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.18), residues: 2128 helix: 1.48 (0.18), residues: 815 sheet: -0.60 (0.31), residues: 281 loop : -1.34 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 773 HIS 0.004 0.001 HIS 3 346 PHE 0.022 0.002 PHE 2 67 TYR 0.018 0.001 TYR 2 419 ARG 0.004 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.04329 ( 687) hydrogen bonds : angle 4.22388 ( 1992) SS BOND : bond 0.00243 ( 18) SS BOND : angle 0.93097 ( 36) covalent geometry : bond 0.00440 (16119) covalent geometry : angle 0.58275 (21997) *********************** 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 278 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 263 time to evaluate : 1.343 Fit side-chains revert: symmetry clash REVERT: 2 168 THR cc_start: 0.8786 (m) cc_final: 0.8458 (m) REVERT: 2 794 MET cc_start: 0.8403 (tpp) cc_final: 0.8061 (mmm) REVERT: B 337 LYS cc_start: 0.5966 (tptt) cc_final: 0.5762 (tptt) outliers start: 15 outliers final: 11 residues processed: 268 average time/residue: 0.2688 time to fit residues: 108.2877 Evaluate side-chains 246 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 235 time to evaluate : 1.603 ------------------------------------------------------------------------------- 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 782 VAL Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 783 LEU 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 137 optimal weight: 3.9990 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 0.3980 chunk 59 optimal weight: 5.9990 chunk 160 optimal weight: 0.7980 chunk 134 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 157 optimal weight: 0.0570 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 197 GLN 3 408 GLN A 346 ASN B 13 GLN B 119 ASN ** 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 = 0.4554 r_free = 0.4554 target = 0.233938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.210531 restraints weight = 18018.489| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 1.25 r_work: 0.4131 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.4098 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6828 moved from start: 0.1999 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= 0.126 Angle : 0.519 9.030 22033 Z= 0.265 Chirality : 0.041 0.141 2572 Planarity : 0.003 0.060 2800 Dihedral : 6.781 83.165 2557 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.07 % Allowed : 12.27 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.18), residues: 2128 helix: 1.60 (0.18), residues: 815 sheet: -0.55 (0.31), residues: 275 loop : -1.30 (0.19), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 773 HIS 0.005 0.000 HIS 3 346 PHE 0.015 0.001 PHE A 199 TYR 0.028 0.001 TYR 3 776 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 687) hydrogen bonds : angle 3.95191 ( 1992) SS BOND : bond 0.00154 ( 18) SS BOND : angle 0.90307 ( 36) covalent geometry : bond 0.00289 (16119) covalent geometry : angle 0.51793 (21997) *********************** 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 262 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 246 time to evaluate : 1.659 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 146 ASP cc_start: 0.7225 (OUTLIER) cc_final: 0.6992 (p0) REVERT: 2 794 MET cc_start: 0.8255 (tpp) cc_final: 0.7960 (mmm) outliers start: 16 outliers final: 11 residues processed: 252 average time/residue: 0.2677 time to fit residues: 101.8212 Evaluate side-chains 239 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 227 time to evaluate : 1.688 ------------------------------------------------------------------------------- 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 622 ILE Chi-restraints excluded: chain 2 residue 760 LYS 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 B residue 99 TRP Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 180 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 125 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 53 optimal weight: 6.9990 chunk 148 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 126 optimal weight: 4.9990 chunk 196 optimal weight: 20.0000 chunk 46 optimal weight: 0.0020 chunk 120 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.9594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 374 GLN ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 13 GLN ** B 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.230863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.215229 restraints weight = 18149.629| |-----------------------------------------------------------------------------| r_work (start): 0.4385 rms_B_bonded: 0.86 r_work: 0.4233 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 2.20 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 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 : 0.004 0.051 16137 Z= 0.172 Angle : 0.556 9.011 22033 Z= 0.287 Chirality : 0.042 0.147 2572 Planarity : 0.004 0.043 2800 Dihedral : 6.606 70.271 2557 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.00 % Allowed : 13.73 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2128 helix: 1.48 (0.18), residues: 816 sheet: -0.65 (0.31), residues: 276 loop : -1.29 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 773 HIS 0.005 0.001 HIS 3 346 PHE 0.019 0.001 PHE 2 67 TYR 0.020 0.001 TYR 2 781 ARG 0.006 0.000 ARG B 52 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 687) hydrogen bonds : angle 4.04014 ( 1992) SS BOND : bond 0.00243 ( 18) SS BOND : angle 0.83911 ( 36) covalent geometry : bond 0.00409 (16119) covalent geometry : angle 0.55576 (21997) *********************** 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 262 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 232 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 146 ASP cc_start: 0.7198 (OUTLIER) cc_final: 0.6973 (p0) REVERT: 2 794 MET cc_start: 0.8189 (tpp) cc_final: 0.7935 (tpp) outliers start: 30 outliers final: 20 residues processed: 248 average time/residue: 0.2749 time to fit residues: 103.2332 Evaluate side-chains 248 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 227 time to evaluate : 1.714 ------------------------------------------------------------------------------- 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 622 ILE Chi-restraints excluded: chain 2 residue 737 LEU Chi-restraints excluded: chain 2 residue 744 LEU Chi-restraints excluded: chain 2 residue 771 ILE 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 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 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 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 25 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 175 optimal weight: 20.0000 chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 199 optimal weight: 0.9990 chunk 8 optimal weight: 0.4980 chunk 10 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 13 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.232759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.218059 restraints weight = 18291.548| |-----------------------------------------------------------------------------| r_work (start): 0.4413 rms_B_bonded: 0.83 r_work: 0.4269 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.4234 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16137 Z= 0.137 Angle : 0.523 8.835 22033 Z= 0.269 Chirality : 0.041 0.139 2572 Planarity : 0.003 0.041 2800 Dihedral : 6.258 58.815 2557 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 2.27 % Allowed : 15.27 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.18), residues: 2128 helix: 1.52 (0.18), residues: 819 sheet: -0.71 (0.31), residues: 276 loop : -1.29 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP 2 773 HIS 0.003 0.000 HIS 3 346 PHE 0.015 0.001 PHE 2 269 TYR 0.011 0.001 TYR 2 419 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 687) hydrogen bonds : angle 3.96419 ( 1992) SS BOND : bond 0.00187 ( 18) SS BOND : angle 0.74587 ( 36) covalent geometry : bond 0.00321 (16119) covalent geometry : angle 0.52272 (21997) *********************** 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 272 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 238 time to evaluate : 1.705 Fit side-chains revert: symmetry clash REVERT: 2 794 MET cc_start: 0.8170 (tpp) cc_final: 0.7789 (mmm) REVERT: 3 285 ILE cc_start: 0.7686 (OUTLIER) cc_final: 0.7275 (tp) REVERT: B 133 VAL cc_start: 0.5756 (OUTLIER) cc_final: 0.5167 (m) outliers start: 34 outliers final: 24 residues processed: 252 average time/residue: 0.2743 time to fit residues: 103.9562 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 : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 744 LEU Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 771 ILE 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 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 A residue 38 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 194 LEU 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 322 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 22 optimal weight: 0.3980 chunk 150 optimal weight: 0.5980 chunk 51 optimal weight: 7.9990 chunk 198 optimal weight: 40.0000 chunk 26 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 7 optimal weight: 0.5980 chunk 186 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 322 HIS 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 = 0.4508 r_free = 0.4508 target = 0.229055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.213558 restraints weight = 18128.846| |-----------------------------------------------------------------------------| r_work (start): 0.4373 rms_B_bonded: 0.85 r_work: 0.4114 rms_B_bonded: 1.23 restraints_weight: 0.5000 r_work: 0.4064 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.4064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6928 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 16137 Z= 0.190 Angle : 0.580 9.047 22033 Z= 0.300 Chirality : 0.043 0.334 2572 Planarity : 0.004 0.043 2800 Dihedral : 6.217 59.881 2557 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.00 % Allowed : 15.73 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.18), residues: 2128 helix: 1.43 (0.18), residues: 812 sheet: -0.79 (0.30), residues: 284 loop : -1.26 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 773 HIS 0.003 0.001 HIS 3 346 PHE 0.019 0.001 PHE 2 67 TYR 0.020 0.001 TYR 2 781 ARG 0.010 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04079 ( 687) hydrogen bonds : angle 4.12944 ( 1992) SS BOND : bond 0.00244 ( 18) SS BOND : angle 0.90868 ( 36) covalent geometry : bond 0.00456 (16119) covalent geometry : angle 0.57959 (21997) *********************** 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 285 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 240 time to evaluate : 1.600 Fit side-chains revert: symmetry clash REVERT: 2 184 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8573 (m) REVERT: 2 365 HIS cc_start: 0.6619 (OUTLIER) cc_final: 0.6104 (m90) REVERT: 3 285 ILE cc_start: 0.7695 (OUTLIER) cc_final: 0.7256 (tp) REVERT: B 79 LEU cc_start: 0.6840 (pp) cc_final: 0.6535 (pp) REVERT: B 133 VAL cc_start: 0.5950 (OUTLIER) cc_final: 0.5282 (m) REVERT: B 333 ASP cc_start: 0.5166 (p0) cc_final: 0.4668 (p0) REVERT: C 21 MET cc_start: 0.4403 (ppp) cc_final: 0.3354 (ppp) outliers start: 45 outliers final: 31 residues processed: 262 average time/residue: 0.2601 time to fit residues: 103.1795 Evaluate side-chains 268 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 1.736 ------------------------------------------------------------------------------- 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 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 634 LEU Chi-restraints excluded: chain 2 residue 691 LEU Chi-restraints excluded: chain 2 residue 737 LEU Chi-restraints excluded: chain 2 residue 744 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 232 GLN 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 629 THR 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 50 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 100 optimal weight: 1.9990 chunk 203 optimal weight: 20.0000 chunk 106 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 179 optimal weight: 7.9990 chunk 101 optimal weight: 0.5980 chunk 72 optimal weight: 0.9990 chunk 201 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN A 346 ASN B 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4518 r_free = 0.4518 target = 0.230194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.214507 restraints weight = 18191.223| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 0.86 r_work: 0.4234 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.4200 rms_B_bonded: 2.19 restraints_weight: 0.2500 r_work (final): 0.4200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16137 Z= 0.146 Angle : 0.555 8.907 22033 Z= 0.284 Chirality : 0.042 0.250 2572 Planarity : 0.004 0.051 2800 Dihedral : 6.063 58.793 2557 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.53 % Allowed : 16.53 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.18), residues: 2128 helix: 1.49 (0.18), residues: 813 sheet: -0.80 (0.30), residues: 294 loop : -1.25 (0.19), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP 2 773 HIS 0.007 0.001 HIS 2 365 PHE 0.017 0.001 PHE 3 652 TYR 0.011 0.001 TYR 2 419 ARG 0.009 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 687) hydrogen bonds : angle 4.03379 ( 1992) SS BOND : bond 0.00192 ( 18) SS BOND : angle 0.72853 ( 36) covalent geometry : bond 0.00343 (16119) covalent geometry : angle 0.55451 (21997) *********************** 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: 38 poor density : 237 time to evaluate : 2.163 Fit side-chains REVERT: 2 168 THR cc_start: 0.8758 (m) cc_final: 0.8539 (m) REVERT: 2 184 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8479 (m) REVERT: 3 285 ILE cc_start: 0.7724 (OUTLIER) cc_final: 0.7321 (tp) REVERT: 3 645 ARG cc_start: 0.7216 (ttp-110) cc_final: 0.6962 (ttp-110) REVERT: B 16 ASN cc_start: 0.5136 (p0) cc_final: 0.4923 (p0) REVERT: B 79 LEU cc_start: 0.6279 (pp) cc_final: 0.6009 (pp) REVERT: B 133 VAL cc_start: 0.5785 (OUTLIER) cc_final: 0.5345 (m) REVERT: B 230 ASN cc_start: 0.5241 (p0) cc_final: 0.4898 (m110) REVERT: B 333 ASP cc_start: 0.4486 (p0) cc_final: 0.4048 (p0) outliers start: 38 outliers final: 30 residues processed: 257 average time/residue: 0.2928 time to fit residues: 113.7987 Evaluate side-chains 267 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 234 time to evaluate : 1.746 ------------------------------------------------------------------------------- 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 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 744 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 285 ILE 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 809 LEU 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 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 322 ASP 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 6 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 132 optimal weight: 0.0870 chunk 96 optimal weight: 1.9990 chunk 144 optimal weight: 0.3980 chunk 177 optimal weight: 4.9990 chunk 135 optimal weight: 0.1980 chunk 205 optimal weight: 10.0000 overall best weight: 0.3758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS A 346 ASN B 13 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.232342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.216860 restraints weight = 18114.026| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 0.89 r_work: 0.4246 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.4214 rms_B_bonded: 2.22 restraints_weight: 0.2500 r_work (final): 0.4214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.2941 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= 0.112 Angle : 0.538 9.335 22033 Z= 0.275 Chirality : 0.041 0.197 2572 Planarity : 0.003 0.044 2800 Dihedral : 5.841 58.856 2557 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.67 % Allowed : 17.00 % Favored : 80.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.18), residues: 2128 helix: 1.64 (0.18), residues: 812 sheet: -0.68 (0.31), residues: 284 loop : -1.22 (0.19), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 3 782 HIS 0.014 0.001 HIS A 188 PHE 0.017 0.001 PHE A 199 TYR 0.008 0.001 TYR 3 256 ARG 0.013 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 687) hydrogen bonds : angle 3.92437 ( 1992) SS BOND : bond 0.00152 ( 18) SS BOND : angle 0.61585 ( 36) covalent geometry : bond 0.00254 (16119) covalent geometry : angle 0.53752 (21997) *********************** 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 283 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 243 time to evaluate : 1.531 Fit side-chains revert: symmetry clash REVERT: 2 168 THR cc_start: 0.8722 (m) cc_final: 0.8354 (m) REVERT: 2 184 THR cc_start: 0.8925 (OUTLIER) cc_final: 0.8365 (m) REVERT: 2 365 HIS cc_start: 0.6167 (OUTLIER) cc_final: 0.5599 (m90) REVERT: 3 285 ILE cc_start: 0.7680 (OUTLIER) cc_final: 0.7303 (tp) REVERT: 3 422 MET cc_start: 0.6794 (OUTLIER) cc_final: 0.6492 (ttt) REVERT: 3 645 ARG cc_start: 0.7232 (ttp-110) cc_final: 0.7021 (ttp-110) REVERT: B 68 ARG cc_start: 0.2244 (tmt170) cc_final: 0.2018 (ttt90) REVERT: B 79 LEU cc_start: 0.6240 (pp) cc_final: 0.5953 (pp) REVERT: B 133 VAL cc_start: 0.5759 (OUTLIER) cc_final: 0.5305 (m) REVERT: B 230 ASN cc_start: 0.5449 (p0) cc_final: 0.5146 (m110) REVERT: C 21 MET cc_start: 0.3866 (ppp) cc_final: 0.2703 (ppp) outliers start: 40 outliers final: 27 residues processed: 262 average time/residue: 0.2910 time to fit residues: 114.1229 Evaluate side-chains 265 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 233 time to evaluate : 1.573 ------------------------------------------------------------------------------- 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 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 744 LEU Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 771 ILE 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 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 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU 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 7 optimal weight: 0.6980 chunk 127 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 192 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 84 optimal weight: 0.0570 chunk 123 optimal weight: 2.9990 chunk 125 optimal weight: 0.6980 chunk 187 optimal weight: 3.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS 2 592 HIS A 22 ASN A 346 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.231543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.215377 restraints weight = 18198.867| |-----------------------------------------------------------------------------| r_work (start): 0.4384 rms_B_bonded: 0.90 r_work: 0.4140 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.4081 rms_B_bonded: 2.21 restraints_weight: 0.2500 r_work (final): 0.4081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16137 Z= 0.136 Angle : 0.565 9.680 22033 Z= 0.288 Chirality : 0.041 0.142 2572 Planarity : 0.004 0.046 2800 Dihedral : 5.812 58.994 2557 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.53 % Allowed : 17.40 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.18), residues: 2128 helix: 1.59 (0.18), residues: 819 sheet: -0.72 (0.31), residues: 285 loop : -1.25 (0.19), residues: 1024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 3 782 HIS 0.010 0.001 HIS 2 365 PHE 0.028 0.001 PHE B 241 TYR 0.043 0.001 TYR 3 776 ARG 0.005 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03608 ( 687) hydrogen bonds : angle 3.97327 ( 1992) SS BOND : bond 0.00169 ( 18) SS BOND : angle 0.63391 ( 36) covalent geometry : bond 0.00320 (16119) covalent geometry : angle 0.56451 (21997) *********************** 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 270 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 1.734 Fit side-chains REVERT: 2 168 THR cc_start: 0.8760 (m) cc_final: 0.8382 (m) REVERT: 2 184 THR cc_start: 0.8940 (OUTLIER) cc_final: 0.8401 (m) REVERT: 2 365 HIS cc_start: 0.6263 (OUTLIER) cc_final: 0.5645 (m170) REVERT: 3 285 ILE cc_start: 0.7643 (OUTLIER) cc_final: 0.7257 (tp) REVERT: 3 422 MET cc_start: 0.6899 (OUTLIER) cc_final: 0.6560 (ttt) REVERT: 3 645 ARG cc_start: 0.7485 (ttp-110) cc_final: 0.7236 (ttp-110) REVERT: B 42 ARG cc_start: 0.5187 (mmp-170) cc_final: 0.4875 (mmp80) REVERT: B 68 ARG cc_start: 0.2135 (tmt170) cc_final: 0.1930 (ttt90) REVERT: B 79 LEU cc_start: 0.6597 (pp) cc_final: 0.6295 (pp) REVERT: B 133 VAL cc_start: 0.5896 (OUTLIER) cc_final: 0.5443 (m) REVERT: B 230 ASN cc_start: 0.6270 (p0) cc_final: 0.5618 (m-40) REVERT: C 21 MET cc_start: 0.4333 (ppp) cc_final: 0.3155 (ppp) outliers start: 38 outliers final: 30 residues processed: 253 average time/residue: 0.2677 time to fit residues: 102.4780 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 : 1.710 ------------------------------------------------------------------------------- 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 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 623 PHE Chi-restraints excluded: chain 2 residue 744 LEU Chi-restraints excluded: chain 2 residue 760 LYS Chi-restraints excluded: chain 2 residue 771 ILE 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 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 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 76 ASP 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 Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 207 optimal weight: 3.9990 chunk 110 optimal weight: 0.9990 chunk 168 optimal weight: 30.0000 chunk 163 optimal weight: 0.9980 chunk 201 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 chunk 157 optimal weight: 4.9990 chunk 142 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 286 ASN 2 365 HIS ** 2 593 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 = 0.4487 r_free = 0.4487 target = 0.226880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.211834 restraints weight = 18108.333| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 0.82 r_work: 0.4211 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.4179 rms_B_bonded: 2.11 restraints_weight: 0.2500 r_work (final): 0.4179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 16137 Z= 0.242 Angle : 0.647 9.949 22033 Z= 0.334 Chirality : 0.045 0.155 2572 Planarity : 0.004 0.047 2800 Dihedral : 6.169 60.503 2557 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.73 % Allowed : 17.40 % Favored : 79.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.18), residues: 2128 helix: 1.29 (0.18), residues: 820 sheet: -0.85 (0.30), residues: 279 loop : -1.27 (0.19), residues: 1029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 3 782 HIS 0.011 0.001 HIS A 188 PHE 0.024 0.002 PHE B 241 TYR 0.017 0.002 TYR 3 434 ARG 0.007 0.001 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 687) hydrogen bonds : angle 4.25942 ( 1992) SS BOND : bond 0.00326 ( 18) SS BOND : angle 0.96085 ( 36) covalent geometry : bond 0.00584 (16119) covalent geometry : angle 0.64676 (21997) ********************** 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 279 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 238 time to evaluate : 1.780 Fit side-chains REVERT: 2 184 THR cc_start: 0.8923 (OUTLIER) cc_final: 0.8532 (m) REVERT: 2 744 LEU cc_start: 0.8410 (OUTLIER) cc_final: 0.8191 (tt) REVERT: 3 285 ILE cc_start: 0.7808 (OUTLIER) cc_final: 0.7367 (tp) REVERT: 3 422 MET cc_start: 0.6839 (OUTLIER) cc_final: 0.6501 (ttt) REVERT: 3 645 ARG cc_start: 0.7296 (ttp-110) cc_final: 0.7057 (ttp-110) REVERT: B 79 LEU cc_start: 0.6099 (pp) cc_final: 0.5829 (pp) REVERT: B 133 VAL cc_start: 0.5791 (OUTLIER) cc_final: 0.5365 (m) REVERT: B 230 ASN cc_start: 0.5670 (p0) cc_final: 0.5462 (m-40) REVERT: C 21 MET cc_start: 0.3790 (ppp) cc_final: 0.2692 (ppp) outliers start: 41 outliers final: 31 residues processed: 259 average time/residue: 0.2616 time to fit residues: 103.1072 Evaluate side-chains 270 residues out of total 1823 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 234 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 273 GLU Chi-restraints excluded: chain 2 residue 325 SER Chi-restraints excluded: chain 2 residue 379 MET Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 623 PHE Chi-restraints excluded: chain 2 residue 737 LEU Chi-restraints excluded: chain 2 residue 744 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 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 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 76 ASP 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 278 PHE Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 42 optimal weight: 0.9980 chunk 138 optimal weight: 0.0270 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 197 optimal weight: 8.9990 chunk 157 optimal weight: 4.9990 chunk 146 optimal weight: 1.9990 chunk 124 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS 2 593 ASN A 346 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.229847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.214635 restraints weight = 18059.339| |-----------------------------------------------------------------------------| r_work (start): 0.4381 rms_B_bonded: 0.85 r_work: 0.4239 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.4207 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.4207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16137 Z= 0.144 Angle : 0.578 10.577 22033 Z= 0.295 Chirality : 0.042 0.142 2572 Planarity : 0.004 0.046 2800 Dihedral : 5.971 59.988 2557 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.47 % Allowed : 18.07 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.18), residues: 2128 helix: 1.44 (0.18), residues: 818 sheet: -0.95 (0.30), residues: 295 loop : -1.26 (0.19), residues: 1015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP 3 782 HIS 0.011 0.001 HIS A 188 PHE 0.027 0.001 PHE B 241 TYR 0.038 0.001 TYR 3 776 ARG 0.008 0.000 ARG B 22 Details of bonding type rmsd hydrogen bonds : bond 0.03770 ( 687) hydrogen bonds : angle 4.06500 ( 1992) SS BOND : bond 0.00176 ( 18) SS BOND : angle 0.70159 ( 36) covalent geometry : bond 0.00337 (16119) covalent geometry : angle 0.57786 (21997) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8299.62 seconds wall clock time: 143 minutes 23.21 seconds (8603.21 seconds total)