Starting phenix.real_space_refine (version: 1.21rc1) on Sat Jul 8 02:34:07 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/07_2023/8jd3_36174_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/07_2023/8jd3_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_36174/07_2023/8jd3_36174.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/07_2023/8jd3_36174.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/07_2023/8jd3_36174_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd3_36174/07_2023/8jd3_36174_neut_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 7.88, per 1000 atoms: 0.50 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: 6.00 Conformation dependent library (CDL) restraints added in 2.5 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: 1.87 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: 4.67 Time building geometry restraints manager: 6.49 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: 8717 17.95 - 35.89: 597 35.89 - 53.84: 124 53.84 - 71.78: 29 71.78 - 89.73: 14 Dihedral angle restraints: 9481 sinusoidal: 3251 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 9478 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: 3.460 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: 11.420 Check model and map are aligned: 0.230 Set scattering table: 0.150 Process input model: 39.540 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.110 ------------------------------------------------------------------------------- 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 : 13.232 89.731 5397 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 % 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 *********************** 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 : 1.664 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 265 average time/residue: 0.2572 time to fit residues: 102.9664 Evaluate side-chains 228 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 227 time to evaluate : 1.694 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1752 time to fit residues: 2.7449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 374 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 16119 Z= 0.326 Angle : 0.592 7.339 21997 Z= 0.304 Chirality : 0.043 0.147 2572 Planarity : 0.004 0.040 2800 Dihedral : 5.948 96.803 2353 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer Outliers : 1.53 % 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: -0.41 (0.18), residues: 2128 helix: 1.16 (0.18), residues: 819 sheet: -0.78 (0.32), residues: 261 loop : -1.33 (0.18), residues: 1048 *********************** 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 275 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 252 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 17 residues processed: 263 average time/residue: 0.2722 time to fit residues: 108.4796 Evaluate side-chains 243 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 226 time to evaluate : 1.661 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1414 time to fit residues: 7.0887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 131 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 192 optimal weight: 20.0000 chunk 208 optimal weight: 30.0000 chunk 171 optimal weight: 20.0000 chunk 191 optimal weight: 8.9990 chunk 65 optimal weight: 7.9990 chunk 154 optimal weight: 9.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 374 GLN 2 655 ASN 3 386 GLN 3 408 GLN 3 688 GLN 3 699 GLN A 322 HIS A 346 ASN 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6746 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.016 0.142 16119 Z= 1.083 Angle : 1.011 13.497 21997 Z= 0.528 Chirality : 0.061 0.365 2572 Planarity : 0.007 0.083 2800 Dihedral : 7.541 119.933 2353 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 13.96 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.04 % Favored : 91.92 % Rotamer Outliers : 2.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -1.70 (0.17), residues: 2128 helix: -0.26 (0.17), residues: 807 sheet: -1.51 (0.29), residues: 285 loop : -1.70 (0.18), residues: 1036 *********************** 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 283 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 241 time to evaluate : 1.724 Fit side-chains revert: symmetry clash outliers start: 42 outliers final: 29 residues processed: 269 average time/residue: 0.2891 time to fit residues: 116.0938 Evaluate side-chains 253 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 224 time to evaluate : 1.785 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 0 residues processed: 29 average time/residue: 0.1688 time to fit residues: 11.1674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 190 optimal weight: 40.0000 chunk 145 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 92 optimal weight: 0.9990 chunk 129 optimal weight: 0.3980 chunk 193 optimal weight: 10.0000 chunk 204 optimal weight: 30.0000 chunk 101 optimal weight: 0.5980 chunk 183 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 365 HIS 2 439 ASN 3 386 GLN A 346 ASN B 13 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: 0.6547 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 16119 Z= 0.227 Angle : 0.567 9.403 21997 Z= 0.293 Chirality : 0.042 0.144 2572 Planarity : 0.004 0.055 2800 Dihedral : 6.214 87.603 2353 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.47 % 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: -1.13 (0.18), residues: 2128 helix: 0.44 (0.18), residues: 806 sheet: -1.27 (0.30), residues: 273 loop : -1.56 (0.18), residues: 1049 *********************** 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 260 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 238 time to evaluate : 1.745 Fit side-chains outliers start: 22 outliers final: 13 residues processed: 249 average time/residue: 0.2795 time to fit residues: 104.2007 Evaluate side-chains 239 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 226 time to evaluate : 1.793 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.1802 time to fit residues: 6.5127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 170 optimal weight: 9.9990 chunk 116 optimal weight: 0.0970 chunk 2 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 84 optimal weight: 0.5980 chunk 174 optimal weight: 8.9990 chunk 141 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 104 optimal weight: 0.0570 chunk 183 optimal weight: 10.0000 chunk 51 optimal weight: 2.9990 overall best weight: 0.7516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 439 ASN 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: 0.6538 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 : 0.003 0.048 16119 Z= 0.228 Angle : 0.552 8.449 21997 Z= 0.284 Chirality : 0.041 0.143 2572 Planarity : 0.004 0.066 2800 Dihedral : 5.901 88.995 2353 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer Outliers : 2.00 % 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: -0.89 (0.18), residues: 2128 helix: 0.75 (0.18), residues: 797 sheet: -1.21 (0.29), residues: 295 loop : -1.48 (0.19), residues: 1036 *********************** 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 271 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 241 time to evaluate : 1.738 Fit side-chains outliers start: 30 outliers final: 17 residues processed: 262 average time/residue: 0.2782 time to fit residues: 109.2150 Evaluate side-chains 242 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 225 time to evaluate : 1.736 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1757 time to fit residues: 7.5833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 68 optimal weight: 1.9990 chunk 184 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 50 optimal weight: 8.9990 chunk 205 optimal weight: 10.0000 chunk 170 optimal weight: 20.0000 chunk 94 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 13 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6586 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.073 16119 Z= 0.350 Angle : 0.601 8.865 21997 Z= 0.307 Chirality : 0.043 0.153 2572 Planarity : 0.004 0.059 2800 Dihedral : 6.107 97.261 2353 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer Outliers : 1.40 % 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: -0.96 (0.18), residues: 2128 helix: 0.65 (0.18), residues: 807 sheet: -1.30 (0.29), residues: 290 loop : -1.48 (0.19), residues: 1031 *********************** 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 254 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 233 time to evaluate : 1.650 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 241 average time/residue: 0.3128 time to fit residues: 115.8723 Evaluate side-chains 240 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 228 time to evaluate : 1.719 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.1607 time to fit residues: 6.0295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 116 optimal weight: 0.0370 chunk 149 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 114 optimal weight: 0.0470 chunk 204 optimal weight: 9.9990 chunk 127 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 chunk 126 optimal weight: 3.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.6531 moved from start: 0.3524 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= 0.214 Angle : 0.550 9.425 21997 Z= 0.279 Chirality : 0.041 0.135 2572 Planarity : 0.004 0.053 2800 Dihedral : 5.736 89.275 2353 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer Outliers : 1.60 % 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: -0.80 (0.18), residues: 2128 helix: 0.85 (0.18), residues: 801 sheet: -1.22 (0.29), residues: 284 loop : -1.44 (0.19), residues: 1043 *********************** 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 261 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 237 time to evaluate : 1.699 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 19 residues processed: 247 average time/residue: 0.2732 time to fit residues: 101.4040 Evaluate side-chains 246 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 227 time to evaluate : 1.680 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1482 time to fit residues: 7.5018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 61 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 129 optimal weight: 10.0000 chunk 139 optimal weight: 10.0000 chunk 101 optimal weight: 0.0670 chunk 19 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 185 optimal weight: 0.0040 overall best weight: 0.6134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 688 GLN ** 3 799 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 ASN B 44 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: 0.6519 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 16119 Z= 0.200 Angle : 0.550 10.753 21997 Z= 0.277 Chirality : 0.041 0.151 2572 Planarity : 0.004 0.087 2800 Dihedral : 5.573 87.299 2353 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer Outliers : 1.00 % 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: -0.76 (0.18), residues: 2128 helix: 0.88 (0.18), residues: 802 sheet: -1.11 (0.30), residues: 284 loop : -1.44 (0.19), residues: 1042 *********************** 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 247 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 232 time to evaluate : 1.742 Fit side-chains outliers start: 15 outliers final: 9 residues processed: 241 average time/residue: 0.2832 time to fit residues: 102.4117 Evaluate side-chains 235 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 226 time to evaluate : 1.551 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1550 time to fit residues: 4.8787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 212 random chunks: chunk 195 optimal weight: 20.0000 chunk 178 optimal weight: 5.9990 chunk 190 optimal weight: 40.0000 chunk 114 optimal weight: 0.9980 chunk 82 optimal weight: 3.9990 chunk 149 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 172 optimal weight: 0.0670 chunk 180 optimal weight: 10.0000 chunk 189 optimal weight: 7.9990 chunk 125 optimal weight: 0.3980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 688 GLN A 346 ASN B 13 GLN B 44 GLN B 119 ASN ** 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: 0.6510 moved from start: 0.3493 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= 0.198 Angle : 0.558 11.493 21997 Z= 0.278 Chirality : 0.041 0.140 2572 Planarity : 0.004 0.050 2800 Dihedral : 5.481 86.272 2353 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer Outliers : 0.33 % 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: -0.70 (0.18), residues: 2128 helix: 0.93 (0.18), residues: 802 sheet: -1.07 (0.30), residues: 285 loop : -1.41 (0.19), residues: 1041 *********************** 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 235 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 230 time to evaluate : 1.692 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 232 average time/residue: 0.2904 time to fit residues: 100.4171 Evaluate side-chains 227 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 224 time to evaluate : 1.772 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1465 time to fit residues: 3.2982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0050 chunk 95 optimal weight: 1.9990 chunk 139 optimal weight: 9.9990 chunk 211 optimal weight: 20.0000 chunk 194 optimal weight: 7.9990 chunk 168 optimal weight: 20.0000 chunk 17 optimal weight: 2.9990 chunk 129 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 chunk 133 optimal weight: 0.9980 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 688 GLN B 13 GLN B 44 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: 0.6580 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 16119 Z= 0.355 Angle : 0.621 12.610 21997 Z= 0.313 Chirality : 0.043 0.150 2572 Planarity : 0.004 0.061 2800 Dihedral : 5.887 95.540 2353 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer Outliers : 0.47 % 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: -0.85 (0.18), residues: 2128 helix: 0.73 (0.18), residues: 805 sheet: -1.22 (0.30), residues: 285 loop : -1.41 (0.19), residues: 1038 ********************** 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 235 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 1.668 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 232 average time/residue: 0.2882 time to fit residues: 100.6756 Evaluate side-chains 228 residues out of total 1823 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 223 time to evaluate : 1.683 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1629 time to fit residues: 4.0127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 155 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 46 optimal weight: 8.9990 chunk 168 optimal weight: 20.0000 chunk 70 optimal weight: 4.9990 chunk 172 optimal weight: 20.0000 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 735 ASN 3 386 GLN 3 688 GLN B 13 GLN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.223163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.201703 restraints weight = 18129.223| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 1.13 r_work: 0.4093 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.4055 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6936 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.090 16119 Z= 0.533 Angle : 0.723 13.779 21997 Z= 0.367 Chirality : 0.047 0.175 2572 Planarity : 0.005 0.062 2800 Dihedral : 6.468 101.908 2353 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.52 % Favored : 92.48 % Rotamer Outliers : 0.33 % 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: -1.18 (0.18), residues: 2128 helix: 0.38 (0.18), residues: 809 sheet: -1.31 (0.30), residues: 284 loop : -1.56 (0.19), residues: 1035 =============================================================================== Job complete usr+sys time: 3264.52 seconds wall clock time: 59 minutes 54.30 seconds (3594.30 seconds total)