Starting phenix.real_space_refine on Tue Apr 9 07:56:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/04_2024/8jd3_36174_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/04_2024/8jd3_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/04_2024/8jd3_36174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/04_2024/8jd3_36174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/04_2024/8jd3_36174_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/04_2024/8jd3_36174_neut_updated.pdb" } 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 Residue "2 GLU 239": "OE1" <-> "OE2" Residue "2 ASP 335": "OD1" <-> "OD2" Residue "2 PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 747": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 761": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 PHE 810": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ASP 221": "OD1" <-> "OD2" Residue "3 TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 28": "OE1" <-> "OE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A GLU 297": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 GLU 901": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 15770 Number of models: 1 Model: "" Number of chains: 7 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: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'CLR': 2, 'PEF': 1} Classifications: {'peptide': 1, 'undetermined': 3} Modifications used: {'COO': 1} Link IDs: {None: 3} Time building chain proxies: 8.40, per 1000 atoms: 0.53 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 - 3.50 Amino acid : False - 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: 5.97 Conformation dependent library (CDL) restraints added in 2.9 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... running ksdssp... Secondary structure from input PDB file: 56 helices and 17 sheets defined 38.1% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.15 Creating SS restraints... Processing helix chain '2' and resid 60 through 74 Processing helix chain '2' and resid 95 through 107 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) Processing helix chain '2' and resid 145 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 170 through 173 removed outlier: 3.693A pdb=" N SER 2 173 " --> pdb=" O ALA 2 170 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 170 through 173' Processing helix chain '2' and resid 188 through 201 removed outlier: 3.774A pdb=" N LYS 2 193 " --> pdb=" O PHE 2 189 " (cutoff:3.500A) Processing helix chain '2' and resid 217 through 230 removed outlier: 3.950A pdb=" N ALA 2 230 " --> pdb=" O LEU 2 226 " (cutoff:3.500A) Processing helix chain '2' and resid 247 through 259 Processing helix chain '2' and resid 272 through 284 Processing helix chain '2' and resid 325 through 332 removed outlier: 3.664A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 343 through 353 removed outlier: 4.568A pdb=" N GLU 2 347 " --> pdb=" O PRO 2 343 " (cutoff:3.500A) Processing helix chain '2' and resid 357 through 359 No H-bonds generated for 'chain '2' and resid 357 through 359' Processing helix chain '2' and resid 376 through 399 removed outlier: 4.434A pdb=" N MET 2 379 " --> pdb=" O SER 2 376 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE 2 380 " --> pdb=" O LYS 2 377 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N HIS 2 390 " --> pdb=" O ALA 2 387 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA 2 391 " --> pdb=" O MET 2 388 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASN 2 394 " --> pdb=" O ALA 2 391 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N MET 2 395 " --> pdb=" O LEU 2 392 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N HIS 2 396 " --> pdb=" O HIS 2 393 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU 2 399 " --> pdb=" O HIS 2 396 " (cutoff:3.500A) Processing helix chain '2' and resid 408 through 410 No H-bonds generated for 'chain '2' and resid 408 through 410' Processing helix chain '2' and resid 415 through 421 Processing helix chain '2' and resid 569 through 591 Processing helix chain '2' and resid 596 through 601 removed outlier: 3.762A pdb=" N SER 2 601 " --> pdb=" O VAL 2 597 " (cutoff:3.500A) Processing helix chain '2' and resid 605 through 623 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 629 through 662 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 678 through 700 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) Processing helix chain '2' and resid 725 through 746 removed outlier: 4.125A pdb=" N MET 2 728 " --> pdb=" O ASP 2 725 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLY 2 730 " --> pdb=" O SER 2 727 " (cutoff:3.500A) Processing helix chain '2' and resid 763 through 783 Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 789 through 809 Processing helix chain '2' and resid 811 through 818 Processing helix chain '3' and resid 67 through 81 Processing helix chain '3' and resid 102 through 111 removed outlier: 3.576A pdb=" N LEU 3 110 " --> pdb=" O LEU 3 106 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N GLU 3 111 " --> pdb=" O GLU 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 151 through 163 removed outlier: 4.274A pdb=" N LEU 3 163 " --> pdb=" O ASN 3 159 " (cutoff:3.500A) Processing helix chain '3' and resid 194 through 207 Processing helix chain '3' and resid 223 through 236 Processing helix chain '3' and resid 258 through 265 Processing helix chain '3' and resid 278 through 291 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 331 through 338 Processing helix chain '3' and resid 349 through 358 removed outlier: 4.547A pdb=" N ASP 3 353 " --> pdb=" O PRO 3 349 " (cutoff:3.500A) Processing helix chain '3' and resid 390 through 411 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) Processing helix chain '3' and resid 420 through 422 No H-bonds generated for 'chain '3' and resid 420 through 422' Processing helix chain '3' and resid 427 through 432 Processing helix chain '3' and resid 450 through 452 No H-bonds generated for 'chain '3' and resid 450 through 452' Processing helix chain '3' and resid 494 through 496 No H-bonds generated for 'chain '3' and resid 494 through 496' Processing helix chain '3' and resid 575 through 601 removed outlier: 4.217A pdb=" N GLY 3 579 " --> pdb=" O ALA 3 575 " (cutoff:3.500A) Proline residue: 3 580 - end of helix Processing helix chain '3' and resid 612 through 633 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 638 through 665 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) Processing helix chain '3' and resid 685 through 709 removed outlier: 3.656A pdb=" N GLN 3 699 " --> pdb=" O LEU 3 695 " (cutoff:3.500A) Processing helix chain '3' and resid 734 through 760 removed outlier: 4.902A pdb=" N LYS 3 760 " --> pdb=" O PHE 3 756 " (cutoff:3.500A) Processing helix chain '3' and resid 768 through 794 Proline residue: 3 787 - end of helix removed outlier: 5.743A pdb=" N SER 3 794 " --> pdb=" O TYR 3 790 " (cutoff:3.500A) Processing helix chain '3' and resid 796 through 828 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 32 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) Processing helix chain 'A' and resid 191 through 193 No H-bonds generated for 'chain 'A' and resid 191 through 193' Processing helix chain 'A' and resid 208 through 215 removed outlier: 4.126A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 273 through 280 removed outlier: 3.699A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 307 Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.877A pdb=" N THR A 316 " --> pdb=" O LYS A 312 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 312 through 316' Processing helix chain 'A' and resid 332 through 349 Processing helix chain 'B' and resid 5 through 35 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) 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 33 through 40 Processing helix chain 'C' and resid 48 through 52 Processing sheet with id= A, 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: 6.805A pdb=" N GLY 2 35 " --> pdb=" O THR 2 137 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N VAL 2 139 " --> pdb=" O GLY 2 35 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU 2 37 " --> pdb=" O VAL 2 139 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N GLY 2 141 " --> pdb=" O LEU 2 37 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N GLY 2 141 " --> pdb=" O PRO 2 161 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ILE 2 163 " --> pdb=" O GLY 2 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 238 through 241 removed outlier: 6.816A pdb=" N THR 2 209 " --> pdb=" O GLU 2 239 " (cutoff:3.500A) removed outlier: 8.234A pdb=" N VAL 2 241 " --> pdb=" O THR 2 209 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA 2 211 " --> pdb=" O VAL 2 241 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N SER 2 208 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL 2 292 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 315 through 319 Processing sheet with id= D, first strand: chain '2' and resid 706 through 708 removed outlier: 3.562A pdb=" N THR 2 718 " --> pdb=" O GLU 2 708 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '3' and resid 91 through 97 removed outlier: 6.482A pdb=" N LEU 3 39 " --> pdb=" O GLY 3 92 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS 3 94 " --> pdb=" O LEU 3 39 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N LEU 3 41 " --> pdb=" O HIS 3 94 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LEU 3 96 " --> pdb=" O LEU 3 41 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N GLY 3 43 " --> pdb=" O LEU 3 96 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY 3 42 " --> pdb=" O ALA 3 143 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N VAL 3 145 " --> pdb=" O GLY 3 42 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N LEU 3 44 " --> pdb=" O VAL 3 145 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain '3' and resid 244 through 247 removed outlier: 6.838A pdb=" N THR 3 215 " --> pdb=" O GLU 3 245 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N VAL 3 247 " --> pdb=" O THR 3 215 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ALA 3 217 " --> pdb=" O VAL 3 247 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N THR 3 296 " --> pdb=" O VAL 3 272 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N LEU 3 274 " --> pdb=" O THR 3 296 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL 3 298 " --> pdb=" O LEU 3 274 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N ALA 3 320 " --> pdb=" O PHE 3 471 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY 3 484 " --> pdb=" O VAL 3 468 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ASN 3 470 " --> pdb=" O LYS 3 482 " (cutoff:3.500A) removed outlier: 5.478A pdb=" N LYS 3 482 " --> pdb=" O ASN 3 470 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N GLN 3 472 " --> pdb=" O TYR 3 480 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N TYR 3 480 " --> pdb=" O GLN 3 472 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL 3 474 " --> pdb=" O TYR 3 478 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N TYR 3 478 " --> pdb=" O VAL 3 474 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '3' and resid 439 through 441 Processing sheet with id= H, first strand: chain '3' and resid 518 through 521 Processing sheet with id= I, 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= I Processing sheet with id= J, first strand: chain 'A' and resid 38 through 40 removed outlier: 8.403A pdb=" N LEU A 39 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N ILE A 222 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N SER A 263 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N PHE A 223 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 186 through 189 Processing sheet with id= L, first strand: chain 'B' and resid 70 through 73 Processing sheet with id= M, first strand: chain 'B' and resid 121 through 125 removed outlier: 3.544A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing sheet with id= N, 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= O, first strand: chain 'B' and resid 198 through 201 Processing sheet with id= P, first strand: chain 'B' and resid 276 through 278 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: 5.384A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 336 through 339 removed outlier: 4.494A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) 604 hydrogen bonds defined for protein. 1689 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 6.44 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: 98.51 - 105.62: 299 105.62 - 112.73: 8631 112.73 - 119.84: 5083 119.84 - 126.95: 7798 126.95 - 134.06: 186 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: 1571 2.75 - 3.29: 15527 3.29 - 3.82: 25904 3.82 - 4.36: 28910 4.36 - 4.90: 50581 Nonbonded interactions: 122493 Sorted by model distance: nonbonded pdb=" O LEU B 168 " pdb=" OG1 THR B 177 " model vdw 2.210 2.440 nonbonded pdb=" OG SER B 147 " pdb=" O MET B 188 " model vdw 2.256 2.440 nonbonded pdb=" O ALA B 56 " pdb=" OG SER B 334 " model vdw 2.258 2.440 nonbonded pdb=" O GLN B 9 " pdb=" NE2 GLN B 13 " model vdw 2.283 2.520 nonbonded pdb=" O LYS A 209 " pdb=" ND1 HIS A 213 " model vdw 2.284 2.520 ... (remaining 122488 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 3.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 10.760 Check model and map are aligned: 0.220 Set scattering table: 0.150 Process input model: 42.100 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.070 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.050 ------------------------------------------------------------------------------- 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 16119 Z= 0.298 Angle : 0.534 15.624 21997 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 264 time to evaluate : 1.748 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: 0.2690 time to fit residues: 108.1285 Evaluate side-chains 228 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.835 ------------------------------------------------------------------------------- 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: 0.7980 chunk 89 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 85 optimal weight: 0.5980 chunk 166 optimal weight: 10.0000 chunk 64 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 123 optimal weight: 5.9990 chunk 192 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 56 HIS 2 374 GLN 2 592 HIS ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 338 GLN ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 470 ASN ** 3 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16119 Z= 0.325 Angle : 0.587 7.345 21997 Z= 0.302 Chirality : 0.043 0.146 2572 Planarity : 0.004 0.040 2800 Dihedral : 7.163 87.031 2560 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.53 % Allowed : 9.00 % Favored : 89.47 % 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: -0.37 (0.18), residues: 2128 helix: 1.23 (0.18), residues: 817 sheet: -0.74 (0.32), residues: 260 loop : -1.33 (0.18), residues: 1051 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 2 773 HIS 0.003 0.001 HIS 2 41 PHE 0.023 0.002 PHE 2 67 TYR 0.020 0.001 TYR 2 419 ARG 0.004 0.000 ARG B 22 *********************** 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 276 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 253 time to evaluate : 1.708 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 159 GLN cc_start: 0.7935 (mm-40) cc_final: 0.7703 (mm110) REVERT: 2 168 THR cc_start: 0.8794 (m) cc_final: 0.8423 (m) REVERT: 2 794 MET cc_start: 0.7984 (tpp) cc_final: 0.7741 (mmm) REVERT: B 19 ARG cc_start: 0.5202 (mmm160) cc_final: 0.5000 (mmp-170) REVERT: B 133 VAL cc_start: 0.5321 (p) cc_final: 0.4889 (m) outliers start: 23 outliers final: 18 residues processed: 264 average time/residue: 0.2812 time to fit residues: 111.8553 Evaluate side-chains 248 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 230 time to evaluate : 1.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 56 HIS Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 333 SER Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 782 VAL Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 783 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 228 ASP 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 106 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 160 optimal weight: 0.7980 chunk 131 optimal weight: 8.9990 chunk 53 optimal weight: 4.9990 chunk 192 optimal weight: 30.0000 chunk 208 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 191 optimal weight: 10.0000 chunk 65 optimal weight: 0.0570 chunk 154 optimal weight: 9.9990 overall best weight: 2.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 374 GLN 3 386 GLN 3 408 GLN 3 688 GLN A 322 HIS B 13 GLN ** B 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.101 16119 Z= 0.698 Angle : 0.784 10.169 21997 Z= 0.408 Chirality : 0.051 0.275 2572 Planarity : 0.006 0.059 2800 Dihedral : 7.376 70.564 2557 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.80 % Allowed : 12.80 % Favored : 84.40 % 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: -1.14 (0.17), residues: 2128 helix: 0.31 (0.18), residues: 816 sheet: -1.10 (0.31), residues: 266 loop : -1.51 (0.18), residues: 1046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP 3 303 HIS 0.012 0.001 HIS 2 56 PHE 0.033 0.003 PHE 2 380 TYR 0.036 0.003 TYR 2 458 ARG 0.007 0.001 ARG 2 183 *********************** 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 284 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 242 time to evaluate : 1.699 Fit side-chains revert: symmetry clash REVERT: 2 239 GLU cc_start: 0.7349 (mp0) cc_final: 0.7112 (mm-30) REVERT: 2 240 LYS cc_start: 0.8370 (mptt) cc_final: 0.7989 (mptt) REVERT: 2 286 ASN cc_start: 0.7108 (m-40) cc_final: 0.6881 (m-40) REVERT: 2 365 HIS cc_start: 0.6337 (OUTLIER) cc_final: 0.5929 (m90) REVERT: 3 285 ILE cc_start: 0.7637 (OUTLIER) cc_final: 0.7197 (tp) REVERT: 3 518 MET cc_start: 0.5573 (ptm) cc_final: 0.5358 (ptm) REVERT: B 333 ASP cc_start: 0.4894 (p0) cc_final: 0.4552 (p0) outliers start: 42 outliers final: 32 residues processed: 270 average time/residue: 0.2922 time to fit residues: 117.1012 Evaluate side-chains 262 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 228 time to evaluate : 1.664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 333 SER Chi-restraints excluded: chain 2 residue 356 SER Chi-restraints excluded: chain 2 residue 365 HIS Chi-restraints excluded: chain 2 residue 437 THR Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 744 LEU 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 102 ASP Chi-restraints excluded: chain 3 residue 173 SER Chi-restraints excluded: chain 3 residue 183 ARG Chi-restraints excluded: chain 3 residue 185 ASP 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 782 TRP Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 20.0000 chunk 204 optimal weight: 30.0000 chunk 101 optimal weight: 0.8980 chunk 183 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 386 GLN A 188 HIS A 346 ASN B 13 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6537 moved from start: 0.3089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 16119 Z= 0.250 Angle : 0.558 8.941 21997 Z= 0.287 Chirality : 0.042 0.151 2572 Planarity : 0.004 0.050 2800 Dihedral : 6.559 65.361 2557 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.13 % Allowed : 16.53 % Favored : 81.33 % 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: -0.88 (0.18), residues: 2128 helix: 0.67 (0.18), residues: 810 sheet: -1.08 (0.30), residues: 263 loop : -1.46 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP 2 773 HIS 0.005 0.001 HIS 2 56 PHE 0.017 0.001 PHE 2 269 TYR 0.019 0.001 TYR 2 781 ARG 0.006 0.000 ARG B 22 *********************** 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 263 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 231 time to evaluate : 1.608 Fit side-chains revert: symmetry clash REVERT: 2 168 THR cc_start: 0.8824 (m) cc_final: 0.8407 (m) REVERT: 2 239 GLU cc_start: 0.7284 (mp0) cc_final: 0.7064 (mm-30) REVERT: 2 286 ASN cc_start: 0.6937 (m-40) cc_final: 0.6712 (m-40) REVERT: B 79 LEU cc_start: 0.6201 (pp) cc_final: 0.5859 (pp) REVERT: B 258 ASP cc_start: 0.5729 (m-30) cc_final: 0.5523 (m-30) outliers start: 32 outliers final: 27 residues processed: 249 average time/residue: 0.2842 time to fit residues: 107.5095 Evaluate side-chains 248 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 221 time to evaluate : 1.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 691 LEU 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 102 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 393 VAL Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 632 PHE Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU 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 170 optimal weight: 0.7980 chunk 116 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 152 optimal weight: 4.9990 chunk 84 optimal weight: 0.8980 chunk 174 optimal weight: 9.9990 chunk 141 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 183 optimal weight: 20.0000 chunk 51 optimal weight: 0.0570 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 699 GLN A 346 ASN B 13 GLN B 119 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16119 Z= 0.206 Angle : 0.529 8.895 21997 Z= 0.271 Chirality : 0.041 0.145 2572 Planarity : 0.004 0.039 2800 Dihedral : 6.076 63.614 2557 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.93 % Allowed : 17.47 % Favored : 79.60 % 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: -0.67 (0.18), residues: 2128 helix: 0.95 (0.18), residues: 801 sheet: -0.95 (0.30), residues: 272 loop : -1.42 (0.18), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 2 773 HIS 0.002 0.000 HIS 2 56 PHE 0.015 0.001 PHE 2 269 TYR 0.015 0.001 TYR 2 473 ARG 0.006 0.000 ARG B 19 *********************** 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 279 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 235 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: 2 168 THR cc_start: 0.8783 (m) cc_final: 0.8401 (m) REVERT: 2 286 ASN cc_start: 0.6769 (m-40) cc_final: 0.6565 (m-40) REVERT: B 45 MET cc_start: 0.1354 (tpt) cc_final: 0.1090 (tpt) REVERT: B 79 LEU cc_start: 0.6222 (pp) cc_final: 0.5938 (pp) outliers start: 44 outliers final: 33 residues processed: 260 average time/residue: 0.2778 time to fit residues: 108.8154 Evaluate side-chains 255 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 2.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 410 MET Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 648 SER 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 2 residue 793 THR Chi-restraints excluded: chain 2 residue 804 VAL Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 393 VAL Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 632 PHE Chi-restraints excluded: chain 3 residue 783 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 228 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 50 optimal weight: 0.0010 chunk 205 optimal weight: 10.0000 chunk 170 optimal weight: 9.9990 chunk 94 optimal weight: 0.6980 chunk 17 optimal weight: 1.9990 chunk 67 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- 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** ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6545 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16119 Z= 0.281 Angle : 0.557 8.635 21997 Z= 0.285 Chirality : 0.042 0.357 2572 Planarity : 0.004 0.046 2800 Dihedral : 6.056 64.881 2557 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 3.60 % Allowed : 17.27 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.18), residues: 2128 helix: 0.87 (0.18), residues: 810 sheet: -1.06 (0.29), residues: 282 loop : -1.39 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP 2 773 HIS 0.002 0.000 HIS 3 405 PHE 0.020 0.001 PHE 2 269 TYR 0.019 0.001 TYR 2 473 ARG 0.004 0.000 ARG B 52 *********************** 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 284 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 230 time to evaluate : 1.887 Fit side-chains REVERT: 2 168 THR cc_start: 0.8724 (m) cc_final: 0.8309 (m) REVERT: 2 184 THR cc_start: 0.8881 (OUTLIER) cc_final: 0.8583 (m) REVERT: 3 285 ILE cc_start: 0.7580 (OUTLIER) cc_final: 0.7181 (tp) REVERT: B 45 MET cc_start: 0.1572 (tpt) cc_final: 0.1297 (tpt) REVERT: B 79 LEU cc_start: 0.6247 (pp) cc_final: 0.5962 (pp) outliers start: 54 outliers final: 40 residues processed: 264 average time/residue: 0.2716 time to fit residues: 109.1290 Evaluate side-chains 266 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 224 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 333 SER Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 648 SER 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 2 residue 793 THR Chi-restraints excluded: chain 2 residue 804 VAL Chi-restraints excluded: chain 2 residue 809 LEU Chi-restraints excluded: chain 2 residue 815 HIS Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 393 VAL Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 632 PHE Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 766 ASN Chi-restraints excluded: chain 3 residue 786 LEU 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 99 TRP Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 197 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 172 optimal weight: 0.4980 chunk 114 optimal weight: 8.9990 chunk 204 optimal weight: 30.0000 chunk 127 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 688 GLN A 346 ASN B 13 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 16119 Z= 0.303 Angle : 0.580 9.026 21997 Z= 0.295 Chirality : 0.042 0.145 2572 Planarity : 0.004 0.047 2800 Dihedral : 6.025 65.451 2557 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 3.40 % Allowed : 17.40 % Favored : 79.20 % 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: -0.71 (0.18), residues: 2128 helix: 0.89 (0.18), residues: 803 sheet: -1.13 (0.29), residues: 282 loop : -1.37 (0.19), residues: 1043 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP 2 773 HIS 0.002 0.000 HIS 3 346 PHE 0.018 0.001 PHE 2 67 TYR 0.024 0.001 TYR 2 473 ARG 0.009 0.000 ARG B 19 *********************** 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 281 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 230 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: 2 168 THR cc_start: 0.8720 (m) cc_final: 0.8305 (m) REVERT: 2 184 THR cc_start: 0.8893 (OUTLIER) cc_final: 0.8591 (m) REVERT: 3 285 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7225 (tp) REVERT: B 79 LEU cc_start: 0.6162 (pp) cc_final: 0.5905 (pp) outliers start: 51 outliers final: 44 residues processed: 260 average time/residue: 0.2769 time to fit residues: 108.7284 Evaluate side-chains 272 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 226 time to evaluate : 1.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 333 SER Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 619 MET Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 648 SER 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 2 residue 804 VAL Chi-restraints excluded: chain 2 residue 815 HIS Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 393 VAL Chi-restraints excluded: chain 3 residue 422 MET Chi-restraints excluded: chain 3 residue 556 THR Chi-restraints excluded: chain 3 residue 601 HIS Chi-restraints excluded: chain 3 residue 629 THR Chi-restraints excluded: chain 3 residue 631 PHE Chi-restraints excluded: chain 3 residue 632 PHE Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 766 ASN Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain 3 residue 813 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 81 optimal weight: 1.9990 chunk 122 optimal weight: 0.7980 chunk 61 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 129 optimal weight: 9.9990 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 0.1980 chunk 19 optimal weight: 1.9990 chunk 160 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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** 3 688 GLN A 346 ASN B 13 GLN B 44 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16119 Z= 0.191 Angle : 0.538 10.365 21997 Z= 0.272 Chirality : 0.041 0.145 2572 Planarity : 0.004 0.047 2800 Dihedral : 5.803 62.710 2557 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.20 % Allowed : 18.27 % Favored : 78.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.58 (0.18), residues: 2128 helix: 1.03 (0.18), residues: 804 sheet: -1.05 (0.30), residues: 282 loop : -1.34 (0.19), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 3 782 HIS 0.002 0.000 HIS 3 346 PHE 0.031 0.001 PHE 3 652 TYR 0.021 0.001 TYR 2 473 ARG 0.008 0.000 ARG B 19 *********************** 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 278 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 230 time to evaluate : 1.742 Fit side-chains REVERT: 2 168 THR cc_start: 0.8805 (m) cc_final: 0.8352 (m) REVERT: 2 184 THR cc_start: 0.8920 (OUTLIER) cc_final: 0.8547 (m) REVERT: 3 285 ILE cc_start: 0.7568 (OUTLIER) cc_final: 0.7235 (tp) REVERT: B 61 MET cc_start: 0.5816 (ppp) cc_final: 0.5551 (ppp) REVERT: B 79 LEU cc_start: 0.6112 (pp) cc_final: 0.5860 (pp) REVERT: B 268 ASN cc_start: 0.3461 (p0) cc_final: 0.1502 (m-40) outliers start: 48 outliers final: 42 residues processed: 259 average time/residue: 0.2838 time to fit residues: 110.3910 Evaluate side-chains 267 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 223 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 619 MET Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 648 SER 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 2 residue 804 VAL Chi-restraints excluded: chain 2 residue 815 HIS Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 393 VAL Chi-restraints excluded: chain 3 residue 415 THR 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 639 VAL Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain B residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 30.0000 chunk 178 optimal weight: 8.9990 chunk 190 optimal weight: 40.0000 chunk 114 optimal weight: 7.9990 chunk 82 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 172 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 125 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** 3 386 GLN 3 688 GLN A 346 ASN ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6601 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 16119 Z= 0.429 Angle : 0.641 10.648 21997 Z= 0.328 Chirality : 0.044 0.159 2572 Planarity : 0.004 0.068 2800 Dihedral : 6.215 66.705 2557 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.72 % Favored : 93.28 % Rotamer: Outliers : 3.73 % Allowed : 18.27 % Favored : 78.00 % 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: -0.85 (0.18), residues: 2128 helix: 0.69 (0.18), residues: 812 sheet: -1.24 (0.30), residues: 286 loop : -1.38 (0.19), residues: 1030 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP 2 773 HIS 0.003 0.001 HIS 3 402 PHE 0.046 0.002 PHE 3 652 TYR 0.039 0.002 TYR 3 776 ARG 0.010 0.001 ARG B 19 *********************** 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 280 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 224 time to evaluate : 1.710 Fit side-chains revert: symmetry clash REVERT: 2 184 THR cc_start: 0.8944 (OUTLIER) cc_final: 0.8701 (m) REVERT: 2 744 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7914 (tt) REVERT: 3 285 ILE cc_start: 0.7672 (OUTLIER) cc_final: 0.7223 (tp) REVERT: B 79 LEU cc_start: 0.6227 (pp) cc_final: 0.5980 (pp) REVERT: B 268 ASN cc_start: 0.3302 (p0) cc_final: 0.1507 (m-40) outliers start: 56 outliers final: 44 residues processed: 260 average time/residue: 0.3093 time to fit residues: 122.6387 Evaluate side-chains 269 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 1.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 273 GLU Chi-restraints excluded: chain 2 residue 333 SER Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 619 MET Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 648 SER 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 2 residue 804 VAL Chi-restraints excluded: chain 2 residue 815 HIS Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 232 GLN Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 393 VAL Chi-restraints excluded: chain 3 residue 415 THR 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 632 PHE Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 766 ASN Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain 3 residue 813 VAL Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU 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 201 optimal weight: 10.0000 chunk 122 optimal weight: 0.6980 chunk 95 optimal weight: 0.9990 chunk 139 optimal weight: 9.9990 chunk 211 optimal weight: 40.0000 chunk 194 optimal weight: 2.9990 chunk 168 optimal weight: 20.0000 chunk 17 optimal weight: 0.6980 chunk 129 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 133 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS ** 2 593 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 688 GLN A 346 ASN B 13 GLN B 44 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16119 Z= 0.241 Angle : 0.566 11.323 21997 Z= 0.289 Chirality : 0.042 0.135 2572 Planarity : 0.004 0.059 2800 Dihedral : 5.921 63.656 2557 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.93 % Allowed : 19.67 % Favored : 77.40 % 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: -0.74 (0.18), residues: 2128 helix: 0.91 (0.18), residues: 801 sheet: -1.25 (0.30), residues: 294 loop : -1.39 (0.19), residues: 1033 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP 3 782 HIS 0.002 0.000 HIS 3 405 PHE 0.027 0.001 PHE B 241 TYR 0.025 0.001 TYR 2 473 ARG 0.010 0.000 ARG B 19 ********************** 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 274 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 230 time to evaluate : 1.864 Fit side-chains revert: symmetry clash REVERT: 2 168 THR cc_start: 0.8861 (m) cc_final: 0.8434 (m) REVERT: 2 184 THR cc_start: 0.8907 (OUTLIER) cc_final: 0.8596 (m) REVERT: 2 744 LEU cc_start: 0.8176 (OUTLIER) cc_final: 0.7870 (tt) REVERT: 3 285 ILE cc_start: 0.7581 (OUTLIER) cc_final: 0.7226 (tp) REVERT: B 79 LEU cc_start: 0.6148 (pp) cc_final: 0.5869 (pp) REVERT: B 268 ASN cc_start: 0.3232 (p0) cc_final: 0.1504 (m-40) outliers start: 44 outliers final: 40 residues processed: 259 average time/residue: 0.3020 time to fit residues: 117.2258 Evaluate side-chains 270 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 227 time to evaluate : 1.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 82 VAL Chi-restraints excluded: chain 2 residue 95 ASP Chi-restraints excluded: chain 2 residue 184 THR Chi-restraints excluded: chain 2 residue 210 VAL Chi-restraints excluded: chain 2 residue 221 ILE Chi-restraints excluded: chain 2 residue 333 SER Chi-restraints excluded: chain 2 residue 433 ARG Chi-restraints excluded: chain 2 residue 479 THR Chi-restraints excluded: chain 2 residue 619 MET Chi-restraints excluded: chain 2 residue 622 ILE Chi-restraints excluded: chain 2 residue 648 SER 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 2 residue 804 VAL Chi-restraints excluded: chain 2 residue 815 HIS Chi-restraints excluded: chain 3 residue 40 VAL Chi-restraints excluded: chain 3 residue 76 ILE Chi-restraints excluded: chain 3 residue 102 ASP Chi-restraints excluded: chain 3 residue 185 ASP Chi-restraints excluded: chain 3 residue 285 ILE Chi-restraints excluded: chain 3 residue 391 MET Chi-restraints excluded: chain 3 residue 393 VAL Chi-restraints excluded: chain 3 residue 415 THR 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 632 PHE Chi-restraints excluded: chain 3 residue 639 VAL Chi-restraints excluded: chain 3 residue 809 LEU Chi-restraints excluded: chain 3 residue 810 SER Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 VAL Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain B residue 99 TRP Chi-restraints excluded: chain B residue 180 PHE Chi-restraints excluded: chain B residue 322 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 336 LEU 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 179 optimal weight: 9.9990 chunk 51 optimal weight: 0.0980 chunk 155 optimal weight: 5.9990 chunk 24 optimal weight: 0.9980 chunk 46 optimal weight: 6.9990 chunk 168 optimal weight: 20.0000 chunk 70 optimal weight: 0.0370 chunk 172 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 147 optimal weight: 1.9990 overall best weight: 1.2262 ------------------------------------------------------------------------------- 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** 2 655 ASN 3 688 GLN A 346 ASN B 13 GLN B 44 GLN ** B 230 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 = 0.4474 r_free = 0.4474 target = 0.225484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.208527 restraints weight = 18046.037| |-----------------------------------------------------------------------------| r_work (start): 0.4324 rms_B_bonded: 0.92 r_work: 0.4207 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.4173 rms_B_bonded: 2.15 restraints_weight: 0.2500 r_work (final): 0.4173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6725 moved from start: 0.3750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 16119 Z= 0.319 Angle : 0.606 11.523 21997 Z= 0.307 Chirality : 0.043 0.146 2572 Planarity : 0.004 0.054 2800 Dihedral : 5.999 65.629 2557 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.20 % Allowed : 19.53 % Favored : 77.27 % 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: -0.77 (0.18), residues: 2128 helix: 0.83 (0.18), residues: 799 sheet: -1.24 (0.29), residues: 302 loop : -1.35 (0.19), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP 3 782 HIS 0.002 0.000 HIS 3 405 PHE 0.025 0.002 PHE 2 269 TYR 0.036 0.002 TYR 3 776 ARG 0.010 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3504.00 seconds wall clock time: 64 minutes 33.94 seconds (3873.94 seconds total)