Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 01:29:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jd5_36176/07_2023/8jd5_36176_neut_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.933 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 120 5.16 5 Cl 1 4.86 5 C 11562 2.51 5 N 3070 2.21 5 O 3274 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "2 GLU 273": "OE1" <-> "OE2" Residue "4 ASP 288": "OD1" <-> "OD2" Residue "4 TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 207": "OE1" <-> "OE2" Residue "A TYR 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 205": "OD1" <-> "OD2" Residue "C ASP 48": "OD1" <-> "OD2" Residue "H PHE 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 GLU 902": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 18028 Number of models: 1 Model: "" Number of chains: 8 Chain: "2" Number of atoms: 5885 Number of conformers: 1 Conformer: "" Number of residues, atoms: 785, 5885 Classifications: {'peptide': 785} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 39, 'TRANS': 745} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 195 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 14, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 183 Chain: "4" Number of atoms: 5804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 765, 5804 Classifications: {'peptide': 765} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 38, 'TRANS': 726} Chain breaks: 4 Unresolved non-hydrogen bonds: 217 Unresolved non-hydrogen angles: 265 Unresolved non-hydrogen dihedrals: 174 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 13, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 129 Chain: "A" Number of atoms: 1644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1644 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 2, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 147 Unresolved non-hydrogen angles: 171 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 9} Unresolved non-hydrogen planarities: 81 Chain: "B" Number of atoms: 2380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2380 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 5, 'TRANS': 328} Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 6, 'ARG:plan': 11, 'ASN:plan1': 4, 'ASP:plan': 10} Unresolved non-hydrogen planarities: 141 Chain: "C" Number of atoms: 334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 334 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "H" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1703 Classifications: {'peptide': 229} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 10, 'TRANS': 218} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 37 Chain: "2" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 179 Unusual residues: {'CLR': 3, 'HZR': 1, 'NAG': 1, 'PEF': 1} Inner-chain residues flagged as termini: ['pdbres="GLU 2 902 "'] Classifications: {'peptide': 1, 'undetermined': 6} Modifications used: {'COO': 1} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Chain: "4" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 99 Unusual residues: {'BQI': 1, 'CLR': 2, 'NAG': 1} Inner-chain residues flagged as termini: ['pdbres="GLU 41002 "'] Classifications: {'peptide': 1, 'undetermined': 4} Modifications used: {'COO': 1} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.77, per 1000 atoms: 0.49 Number of scatterers: 18028 At special positions: 0 Unit cell: (112.455, 126.378, 245.259, 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 120 16.00 P 1 15.00 O 3274 8.00 N 3070 7.00 C 11562 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=2.04 Simple disulfide: pdb=" SG CYS 2 632 " - pdb=" SG CYS 2 721 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 67 " - pdb=" SG CYS 4 109 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 249 " - pdb=" SG CYS 4 538 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 428 " - pdb=" SG CYS 4 435 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 520 " - pdb=" SG CYS 4 539 " distance=2.03 Simple disulfide: pdb=" SG CYS 4 524 " - pdb=" SG CYS 4 542 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 545 " - pdb=" SG CYS 4 557 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 560 " - pdb=" SG CYS 4 573 " distance=2.04 Simple disulfide: pdb=" SG CYS 4 652 " - pdb=" SG CYS 4 746 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 159 " - pdb=" SG CYS H 229 " 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 Links applied NAG-ASN " NAG 2 905 " - " ASN 2 203 " " NAG 41003 " - " ASN 4 454 " Time building additional restraints: 8.58 Conformation dependent library (CDL) restraints added in 3.2 seconds 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4442 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 62 helices and 22 sheets defined 34.2% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain '2' and resid 59 through 73 removed outlier: 3.604A pdb=" N LEU 2 66 " --> pdb=" O LEU 2 62 " (cutoff:3.500A) Processing helix chain '2' and resid 95 through 106 removed outlier: 3.944A pdb=" N LEU 2 103 " --> pdb=" O LEU 2 99 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ASP 2 104 " --> pdb=" O GLU 2 100 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE 2 105 " --> pdb=" O GLN 2 101 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL 2 106 " --> pdb=" O ALA 2 102 " (cutoff:3.500A) Processing helix chain '2' and resid 145 through 157 removed outlier: 3.550A pdb=" N LEU 2 154 " --> pdb=" O GLN 2 150 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU 2 157 " --> pdb=" O ASN 2 153 " (cutoff:3.500A) Processing helix chain '2' and resid 192 through 201 Processing helix chain '2' and resid 217 through 230 Processing helix chain '2' and resid 247 through 259 removed outlier: 3.587A pdb=" N GLU 2 251 " --> pdb=" O ARG 2 247 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL 2 254 " --> pdb=" O PHE 2 250 " (cutoff:3.500A) Processing helix chain '2' and resid 272 through 283 removed outlier: 3.792A pdb=" N ARG 2 276 " --> pdb=" O SER 2 272 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLU 2 277 " --> pdb=" O GLU 2 273 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU 2 278 " --> pdb=" O ASP 2 274 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 332 removed outlier: 3.539A pdb=" N SER 2 329 " --> pdb=" O SER 2 325 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 351 removed outlier: 3.618A pdb=" N GLU 2 350 " --> pdb=" O ARG 2 346 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN 2 351 " --> pdb=" O GLU 2 347 " (cutoff:3.500A) Processing helix chain '2' and resid 378 through 399 removed outlier: 3.899A pdb=" N MET 2 388 " --> pdb=" O ALA 2 384 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA 2 391 " --> pdb=" O ALA 2 387 " (cutoff:3.500A) Processing helix chain '2' and resid 415 through 422 removed outlier: 3.595A pdb=" N LYS 2 420 " --> pdb=" O ARG 2 416 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASP 2 421 " --> pdb=" O ARG 2 417 " (cutoff:3.500A) Processing helix chain '2' and resid 490 through 492 No H-bonds generated for 'chain '2' and resid 490 through 492' Processing helix chain '2' and resid 566 through 568 No H-bonds generated for 'chain '2' and resid 566 through 568' Processing helix chain '2' and resid 570 through 591 Processing helix chain '2' and resid 603 through 623 removed outlier: 3.517A pdb=" N TYR 2 607 " --> pdb=" O ARG 2 603 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE 2 608 " --> pdb=" O GLU 2 604 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE 2 621 " --> pdb=" O TYR 2 617 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ILE 2 622 " --> pdb=" O CYS 2 618 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N PHE 2 623 " --> pdb=" O MET 2 619 " (cutoff:3.500A) Processing helix chain '2' and resid 629 through 661 removed outlier: 3.946A pdb=" N LEU 2 634 " --> pdb=" O ALA 2 630 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ARG 2 636 " --> pdb=" O CYS 2 632 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU 2 637 " --> pdb=" O THR 2 633 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE 2 643 " --> pdb=" O LEU 2 639 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N TYR 2 647 " --> pdb=" O PHE 2 643 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N LEU 2 650 " --> pdb=" O CYS 2 646 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU 2 651 " --> pdb=" O TYR 2 647 " (cutoff:3.500A) Processing helix chain '2' and resid 676 through 700 removed outlier: 3.670A pdb=" N VAL 2 680 " --> pdb=" O PRO 2 676 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ALA 2 681 " --> pdb=" O ALA 2 677 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU 2 686 " --> pdb=" O ILE 2 682 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN 2 690 " --> pdb=" O LEU 2 686 " (cutoff:3.500A) Processing helix chain '2' and resid 729 through 747 removed outlier: 3.542A pdb=" N LEU 2 741 " --> pdb=" O LEU 2 737 " (cutoff:3.500A) Processing helix chain '2' and resid 754 through 756 No H-bonds generated for 'chain '2' and resid 754 through 756' Processing helix chain '2' and resid 759 through 782 removed outlier: 3.970A pdb=" N CYS 2 770 " --> pdb=" O MET 2 766 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU 2 777 " --> pdb=" O TRP 2 773 " (cutoff:3.500A) Proline residue: 2 778 - end of helix Processing helix chain '2' and resid 787 through 818 removed outlier: 3.680A pdb=" N THR 2 792 " --> pdb=" O ARG 2 788 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N MET 2 794 " --> pdb=" O GLN 2 790 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL 2 798 " --> pdb=" O MET 2 794 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER 2 799 " --> pdb=" O CYS 2 795 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA 2 811 " --> pdb=" O GLY 2 807 " (cutoff:3.500A) Proline residue: 2 812 - end of helix removed outlier: 3.723A pdb=" N ILE 2 816 " --> pdb=" O PRO 2 812 " (cutoff:3.500A) Processing helix chain '4' and resid 76 through 89 removed outlier: 3.919A pdb=" N ALA 4 81 " --> pdb=" O HIS 4 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET 4 82 " --> pdb=" O ARG 4 78 " (cutoff:3.500A) Processing helix chain '4' and resid 112 through 121 removed outlier: 3.694A pdb=" N LEU 4 116 " --> pdb=" O ASP 4 112 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU 4 117 " --> pdb=" O THR 4 113 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLN 4 118 " --> pdb=" O HIS 4 114 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR 4 121 " --> pdb=" O GLU 4 117 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 169 removed outlier: 4.050A pdb=" N ILE 4 168 " --> pdb=" O MET 4 164 " (cutoff:3.500A) Processing helix chain '4' and resid 185 through 187 No H-bonds generated for 'chain '4' and resid 185 through 187' Processing helix chain '4' and resid 202 through 215 removed outlier: 3.594A pdb=" N GLN 4 207 " --> pdb=" O THR 4 203 " (cutoff:3.500A) Processing helix chain '4' and resid 231 through 245 removed outlier: 3.647A pdb=" N ALA 4 237 " --> pdb=" O SER 4 233 " (cutoff:3.500A) Processing helix chain '4' and resid 262 through 274 removed outlier: 4.140A pdb=" N ASP 4 266 " --> pdb=" O ALA 4 262 " (cutoff:3.500A) Processing helix chain '4' and resid 287 through 299 removed outlier: 4.096A pdb=" N ARG 4 291 " --> pdb=" O GLU 4 287 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ARG 4 292 " --> pdb=" O ASP 4 288 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ARG 4 298 " --> pdb=" O LEU 4 294 " (cutoff:3.500A) Processing helix chain '4' and resid 312 through 314 No H-bonds generated for 'chain '4' and resid 312 through 314' Processing helix chain '4' and resid 319 through 321 No H-bonds generated for 'chain '4' and resid 319 through 321' Processing helix chain '4' and resid 342 through 348 removed outlier: 3.544A pdb=" N ARG 4 346 " --> pdb=" O ARG 4 342 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR 4 347 " --> pdb=" O GLY 4 343 " (cutoff:3.500A) Processing helix chain '4' and resid 361 through 371 Processing helix chain '4' and resid 395 through 397 No H-bonds generated for 'chain '4' and resid 395 through 397' Processing helix chain '4' and resid 404 through 427 removed outlier: 3.608A pdb=" N GLN 4 407 " --> pdb=" O GLY 4 404 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ASP 4 411 " --> pdb=" O PHE 4 408 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALA 4 412 " --> pdb=" O VAL 4 409 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL 4 413 " --> pdb=" O ILE 4 410 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEU 4 427 " --> pdb=" O HIS 4 424 " (cutoff:3.500A) Processing helix chain '4' and resid 436 through 438 No H-bonds generated for 'chain '4' and resid 436 through 438' Processing helix chain '4' and resid 443 through 452 removed outlier: 3.754A pdb=" N LYS 4 448 " --> pdb=" O THR 4 444 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR 4 449 " --> pdb=" O GLN 4 445 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN 4 452 " --> pdb=" O LYS 4 448 " (cutoff:3.500A) Processing helix chain '4' and resid 586 through 588 No H-bonds generated for 'chain '4' and resid 586 through 588' Processing helix chain '4' and resid 590 through 611 Processing helix chain '4' and resid 618 through 620 No H-bonds generated for 'chain '4' and resid 618 through 620' Processing helix chain '4' and resid 627 through 643 removed outlier: 3.853A pdb=" N THR 4 640 " --> pdb=" O CYS 4 636 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE 4 641 " --> pdb=" O TYR 4 637 " (cutoff:3.500A) Processing helix chain '4' and resid 649 through 686 removed outlier: 3.608A pdb=" N ARG 4 656 " --> pdb=" O CYS 4 652 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE 4 657 " --> pdb=" O SER 4 653 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET 4 663 " --> pdb=" O LEU 4 659 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N SER 4 666 " --> pdb=" O GLY 4 662 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA 4 669 " --> pdb=" O ILE 4 665 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU 4 670 " --> pdb=" O SER 4 666 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG 4 686 " --> pdb=" O GLU 4 682 " (cutoff:3.500A) Processing helix chain '4' and resid 696 through 720 removed outlier: 3.527A pdb=" N LEU 4 700 " --> pdb=" O PRO 4 696 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA 4 701 " --> pdb=" O ALA 4 697 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE 4 702 " --> pdb=" O SER 4 698 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU 4 706 " --> pdb=" O ILE 4 702 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE 4 707 " --> pdb=" O THR 4 703 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN 4 710 " --> pdb=" O LEU 4 706 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N CYS 4 715 " --> pdb=" O LEU 4 711 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL 4 716 " --> pdb=" O LEU 4 712 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N TRP 4 717 " --> pdb=" O GLY 4 713 " (cutoff:3.500A) Processing helix chain '4' and resid 750 through 775 removed outlier: 3.931A pdb=" N SER 4 760 " --> pdb=" O LEU 4 756 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N THR 4 766 " --> pdb=" O LEU 4 762 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N CYS 4 767 " --> pdb=" O LEU 4 763 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG 4 775 " --> pdb=" O ALA 4 771 " (cutoff:3.500A) Processing helix chain '4' and resid 781 through 783 No H-bonds generated for 'chain '4' and resid 781 through 783' Processing helix chain '4' and resid 785 through 799 removed outlier: 3.647A pdb=" N TYR 4 792 " --> pdb=" O GLY 4 788 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL 4 797 " --> pdb=" O THR 4 793 " (cutoff:3.500A) Processing helix chain '4' and resid 802 through 807 Processing helix chain '4' and resid 820 through 846 removed outlier: 3.505A pdb=" N VAL 4 824 " --> pdb=" O THR 4 820 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER 4 833 " --> pdb=" O SER 4 829 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET 4 836 " --> pdb=" O VAL 4 832 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N MET 4 839 " --> pdb=" O GLY 4 835 " (cutoff:3.500A) Proline residue: 4 840 - end of helix Processing helix chain 'A' and resid 7 through 31 removed outlier: 3.881A pdb=" N GLU A 28 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 29 " --> pdb=" O GLU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 209 through 215 removed outlier: 3.987A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 215' Processing helix chain 'A' and resid 242 through 255 removed outlier: 3.599A pdb=" N SER A 246 " --> pdb=" O ARG A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 280 removed outlier: 4.181A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 285 No H-bonds generated for 'chain 'A' and resid 283 through 285' Processing helix chain 'A' and resid 296 through 308 removed outlier: 3.510A pdb=" N PHE A 307 " --> pdb=" O ILE A 303 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N GLU A 308 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 351 removed outlier: 3.597A pdb=" N ASP A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 28 removed outlier: 3.895A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG B 19 " --> pdb=" O LYS B 15 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 26 removed outlier: 3.710A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LYS C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ASP C 26 " --> pdb=" O GLU C 22 " (cutoff:3.500A) Processing helix chain 'C' and resid 32 through 43 Processing helix chain 'H' and resid 53 through 55 No H-bonds generated for 'chain 'H' and resid 53 through 55' Processing helix chain 'H' and resid 62 through 64 No H-bonds generated for 'chain 'H' and resid 62 through 64' Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing sheet with id= A, first strand: chain '2' and resid 87 through 90 removed outlier: 3.667A pdb=" N GLY 2 36 " --> pdb=" O HIS 2 87 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE 2 38 " --> pdb=" O LEU 2 89 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N GLY 2 141 " --> pdb=" O PRO 2 161 " (cutoff:3.500A) removed outlier: 5.376A pdb=" N ILE 2 163 " --> pdb=" O GLY 2 141 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain '2' and resid 239 through 241 removed outlier: 6.603A pdb=" N VAL 2 265 " --> pdb=" O SER 2 208 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N VAL 2 210 " --> pdb=" O VAL 2 265 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL 2 267 " --> pdb=" O VAL 2 210 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER 2 212 " --> pdb=" O VAL 2 267 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N PHE 2 269 " --> pdb=" O SER 2 212 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR 2 290 " --> pdb=" O ALA 2 266 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU 2 268 " --> pdb=" O THR 2 290 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VAL 2 292 " --> pdb=" O LEU 2 268 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N ALA 2 314 " --> pdb=" O TYR 2 458 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N TYR 2 453 " --> pdb=" O TRP 2 474 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY 2 472 " --> pdb=" O ILE 2 455 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR 2 457 " --> pdb=" O LYS 2 470 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS 2 470 " --> pdb=" O THR 2 457 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU 2 459 " --> pdb=" O TYR 2 468 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N TYR 2 468 " --> pdb=" O LEU 2 459 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain '2' and resid 509 through 511 Processing sheet with id= D, first strand: chain '4' and resid 101 through 107 removed outlier: 6.620A pdb=" N ILE 4 49 " --> pdb=" O GLY 4 102 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ARG 4 104 " --> pdb=" O ILE 4 49 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N LEU 4 51 " --> pdb=" O ARG 4 104 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N LEU 4 106 " --> pdb=" O LEU 4 51 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY 4 53 " --> pdb=" O LEU 4 106 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLY 4 52 " --> pdb=" O VAL 4 151 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL 4 153 " --> pdb=" O GLY 4 52 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU 4 54 " --> pdb=" O VAL 4 153 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain '4' and resid 253 through 256 removed outlier: 9.308A pdb=" N VAL 4 254 " --> pdb=" O VAL 4 221 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N THR 4 223 " --> pdb=" O VAL 4 254 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N ILE 4 256 " --> pdb=" O THR 4 223 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N ALA 4 225 " --> pdb=" O ILE 4 256 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ALA 4 280 " --> pdb=" O SER 4 222 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N VAL 4 224 " --> pdb=" O ALA 4 280 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ILE 4 282 " --> pdb=" O VAL 4 224 " (cutoff:3.500A) removed outlier: 8.150A pdb=" N SER 4 226 " --> pdb=" O ILE 4 282 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N PHE 4 284 " --> pdb=" O SER 4 226 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N PHE 4 307 " --> pdb=" O VAL 4 281 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N ILE 4 283 " --> pdb=" O PHE 4 307 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N MET 4 309 " --> pdb=" O ILE 4 283 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain '4' and resid 332 through 336 removed outlier: 3.592A pdb=" N GLY 4 493 " --> pdb=" O ILE 4 477 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N GLN 4 479 " --> pdb=" O VAL 4 491 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N VAL 4 491 " --> pdb=" O GLN 4 479 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N GLN 4 481 " --> pdb=" O TYR 4 489 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N TYR 4 489 " --> pdb=" O GLN 4 481 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain '4' and resid 454 through 456 removed outlier: 3.629A pdb=" N PHE 4 455 " --> pdb=" O VAL 4 463 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain '4' and resid 531 through 533 Processing sheet with id= I, first strand: chain '4' and resid 564 through 566 Processing sheet with id= J, first strand: chain 'A' and resid 36 through 39 removed outlier: 7.921A pdb=" N ALA A 220 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N LEU A 39 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 222 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N SER A 263 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N PHE A 223 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ILE A 265 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N VAL A 225 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE A 267 " --> pdb=" O VAL A 225 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'A' and resid 185 through 191 Processing sheet with id= L, first strand: chain 'B' and resid 91 through 94 removed outlier: 4.012A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'B' and resid 121 through 125 removed outlier: 3.660A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR B 102 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.724A pdb=" N THR B 159 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'B' and resid 207 through 209 Processing sheet with id= P, first strand: chain 'B' and resid 250 through 254 removed outlier: 3.517A pdb=" N ARG B 251 " --> pdb=" O THR B 243 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'B' and resid 284 through 286 removed outlier: 3.616A pdb=" N LEU B 308 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 296 " --> pdb=" O GLY B 306 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'B' and resid 336 through 339 removed outlier: 4.086A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'H' and resid 20 through 23 removed outlier: 3.579A pdb=" N LEU H 81 " --> pdb=" O LEU H 20 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 93 through 99 removed outlier: 4.061A pdb=" N ALA H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.556A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TYR H 50 " --> pdb=" O TYR H 59 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N TYR H 59 " --> pdb=" O TYR H 50 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'H' and resid 155 through 160 removed outlier: 3.701A pdb=" N ALA H 211 " --> pdb=" O SER H 208 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N SER H 208 " --> pdb=" O ALA H 211 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 204 " --> pdb=" O THR H 215 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 174 through 179 removed outlier: 3.586A pdb=" N TYR H 175 " --> pdb=" O MET H 230 " (cutoff:3.500A) 577 hydrogen bonds defined for protein. 1650 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 9.04 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: 2857 1.31 - 1.44: 5100 1.44 - 1.57: 10323 1.57 - 1.70: 7 1.70 - 1.83: 161 Bond restraints: 18448 Sorted by residual: bond pdb=" C11 BQI 41004 " pdb=" N10 BQI 41004 " ideal model delta sigma weight residual 1.564 1.364 0.200 2.00e-02 2.50e+03 9.99e+01 bond pdb=" C12 BQI 41004 " pdb=" S13 BQI 41004 " ideal model delta sigma weight residual 1.516 1.691 -0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" C18 HZR 2 901 " pdb=" C19 HZR 2 901 " ideal model delta sigma weight residual 1.353 1.524 -0.171 2.00e-02 2.50e+03 7.32e+01 bond pdb=" C09 BQI 41004 " pdb=" S13 BQI 41004 " ideal model delta sigma weight residual 1.543 1.689 -0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" C19 HZR 2 901 " pdb=" N20 HZR 2 901 " ideal model delta sigma weight residual 1.353 1.487 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 18443 not shown) Histogram of bond angle deviations from ideal: 96.83 - 104.34: 274 104.34 - 111.84: 8997 111.84 - 119.35: 6278 119.35 - 126.85: 9348 126.85 - 134.36: 256 Bond angle restraints: 25153 Sorted by residual: angle pdb=" C PRO 2 496 " pdb=" N ALA 2 497 " pdb=" CA ALA 2 497 " ideal model delta sigma weight residual 123.03 113.22 9.81 1.79e+00 3.12e-01 3.00e+01 angle pdb=" O3P PEF 2 904 " pdb=" P PEF 2 904 " pdb=" O4P PEF 2 904 " ideal model delta sigma weight residual 93.96 109.42 -15.46 3.00e+00 1.11e-01 2.66e+01 angle pdb=" C PRO 2 261 " pdb=" N SER 2 262 " pdb=" CA SER 2 262 " ideal model delta sigma weight residual 122.65 114.49 8.16 1.60e+00 3.91e-01 2.60e+01 angle pdb=" N LYS 2 260 " pdb=" CA LYS 2 260 " pdb=" C LYS 2 260 " ideal model delta sigma weight residual 108.76 101.60 7.16 1.44e+00 4.82e-01 2.47e+01 angle pdb=" C ARG 2 499 " pdb=" CA ARG 2 499 " pdb=" CB ARG 2 499 " ideal model delta sigma weight residual 109.37 118.41 -9.04 1.83e+00 2.99e-01 2.44e+01 ... (remaining 25148 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.28: 10317 24.28 - 48.57: 421 48.57 - 72.85: 37 72.85 - 97.13: 21 97.13 - 121.42: 2 Dihedral angle restraints: 10798 sinusoidal: 3900 harmonic: 6898 Sorted by residual: dihedral pdb=" CB CYS 2 525 " pdb=" SG CYS 2 525 " pdb=" SG CYS 2 537 " pdb=" CB CYS 2 537 " ideal model delta sinusoidal sigma weight residual 93.00 -177.75 -89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS 4 652 " pdb=" SG CYS 4 652 " pdb=" SG CYS 4 746 " pdb=" CB CYS 4 746 " ideal model delta sinusoidal sigma weight residual 93.00 177.57 -84.57 1 1.00e+01 1.00e-02 8.69e+01 dihedral pdb=" CB CYS 4 520 " pdb=" SG CYS 4 520 " pdb=" SG CYS 4 539 " pdb=" CB CYS 4 539 " ideal model delta sinusoidal sigma weight residual 93.00 175.39 -82.39 1 1.00e+01 1.00e-02 8.33e+01 ... (remaining 10795 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2616 0.071 - 0.143: 268 0.143 - 0.214: 23 0.214 - 0.285: 2 0.285 - 0.357: 2 Chirality restraints: 2911 Sorted by residual: chirality pdb=" CA ASP B 186 " pdb=" N ASP B 186 " pdb=" C ASP B 186 " pdb=" CB ASP B 186 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.18e+00 chirality pdb=" C2 PEF 2 904 " pdb=" C1 PEF 2 904 " pdb=" C3 PEF 2 904 " pdb=" O2 PEF 2 904 " both_signs ideal model delta sigma weight residual False -2.35 -2.68 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA GLU 2 502 " pdb=" N GLU 2 502 " pdb=" C GLU 2 502 " pdb=" CB GLU 2 502 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.33e+00 ... (remaining 2908 not shown) Planarity restraints: 3181 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR B 184 " -0.026 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C THR B 184 " 0.085 2.00e-02 2.50e+03 pdb=" O THR B 184 " -0.031 2.00e-02 2.50e+03 pdb=" N GLY B 185 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU 2 258 " -0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" C LEU 2 258 " 0.053 2.00e-02 2.50e+03 pdb=" O LEU 2 258 " -0.020 2.00e-02 2.50e+03 pdb=" N GLN 2 259 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 208 " -0.270 9.50e-02 1.11e+02 1.21e-01 9.02e+00 pdb=" NE ARG A 208 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 208 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 208 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 208 " -0.009 2.00e-02 2.50e+03 ... (remaining 3178 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1300 2.74 - 3.28: 18228 3.28 - 3.82: 29047 3.82 - 4.36: 33984 4.36 - 4.90: 58446 Nonbonded interactions: 141005 Sorted by model distance: nonbonded pdb=" O LEU A 268 " pdb=" OG1 THR A 324 " model vdw 2.201 2.440 nonbonded pdb=" O GLN 2 790 " pdb=" OG1 THR 2 793 " model vdw 2.215 2.440 nonbonded pdb=" OG1 THR 4 672 " pdb=" OE1 GLN 4 699 " model vdw 2.225 2.440 nonbonded pdb=" O GLY H 112 " pdb=" OG SER H 184 " model vdw 2.225 2.440 nonbonded pdb=" O PRO 2 434 " pdb=" OG1 THR 2 437 " model vdw 2.230 2.440 ... (remaining 141000 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 group one per residue 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: 2.520 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: 11.710 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 48.020 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.090 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 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 : 0.005 0.200 18448 Z= 0.351 Angle : 0.632 15.462 25153 Z= 0.355 Chirality : 0.045 0.357 2911 Planarity : 0.004 0.121 3179 Dihedral : 12.908 121.417 6302 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.73 % Favored : 93.18 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.05 % 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: -0.84 (0.17), residues: 2361 helix: 0.69 (0.19), residues: 753 sheet: 0.16 (0.29), residues: 353 loop : -1.61 (0.17), residues: 1255 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 275 time to evaluate : 1.993 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 281 average time/residue: 0.3350 time to fit residues: 139.1828 Evaluate side-chains 205 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 202 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1615 time to fit residues: 3.6993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.3980 chunk 178 optimal weight: 20.0000 chunk 99 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 120 optimal weight: 0.0030 chunk 95 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 112 optimal weight: 0.5980 chunk 137 optimal weight: 0.0870 chunk 214 optimal weight: 7.9990 overall best weight: 0.3368 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 541 HIS A 204 GLN A 255 ASN H 179 GLN H 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 18448 Z= 0.175 Angle : 0.558 7.945 25153 Z= 0.287 Chirality : 0.041 0.210 2911 Planarity : 0.004 0.055 3179 Dihedral : 5.765 117.929 2660 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer Outliers : 1.18 % 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: -0.73 (0.17), residues: 2361 helix: 0.73 (0.18), residues: 782 sheet: 0.13 (0.29), residues: 356 loop : -1.53 (0.17), residues: 1223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 237 time to evaluate : 2.005 Fit side-chains revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 245 average time/residue: 0.3341 time to fit residues: 122.3961 Evaluate side-chains 208 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 197 time to evaluate : 2.013 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1729 time to fit residues: 6.2751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 178 optimal weight: 20.0000 chunk 145 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 214 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 chunk 212 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 172 optimal weight: 0.5980 overall best weight: 1.0962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 153 ASN 2 191 GLN 2 283 GLN 2 374 GLN ** 2 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 194 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 18448 Z= 0.302 Angle : 0.630 8.268 25153 Z= 0.324 Chirality : 0.044 0.185 2911 Planarity : 0.004 0.059 3179 Dihedral : 6.117 117.992 2660 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 2.01 % 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: -0.90 (0.17), residues: 2361 helix: 0.54 (0.18), residues: 801 sheet: -0.35 (0.26), residues: 400 loop : -1.51 (0.18), residues: 1160 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 222 time to evaluate : 2.041 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 23 residues processed: 242 average time/residue: 0.3312 time to fit residues: 120.5142 Evaluate side-chains 214 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 2.043 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1687 time to fit residues: 10.0715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 10.0000 chunk 161 optimal weight: 2.9990 chunk 111 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 144 optimal weight: 6.9990 chunk 215 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 112 optimal weight: 0.7980 chunk 204 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 2 690 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN ** H 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 18448 Z= 0.314 Angle : 0.612 9.451 25153 Z= 0.313 Chirality : 0.044 0.194 2911 Planarity : 0.004 0.061 3179 Dihedral : 6.192 118.125 2660 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.07 % Favored : 92.93 % Rotamer Outliers : 2.01 % 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: -1.00 (0.17), residues: 2361 helix: 0.49 (0.18), residues: 799 sheet: -0.52 (0.26), residues: 408 loop : -1.56 (0.18), residues: 1154 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 209 time to evaluate : 2.246 Fit side-chains revert: symmetry clash outliers start: 36 outliers final: 23 residues processed: 236 average time/residue: 0.3145 time to fit residues: 113.2123 Evaluate side-chains 213 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 190 time to evaluate : 1.843 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1694 time to fit residues: 9.7376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 169 optimal weight: 8.9990 chunk 94 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 204 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 2 153 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6898 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 18448 Z= 0.283 Angle : 0.604 9.677 25153 Z= 0.306 Chirality : 0.043 0.290 2911 Planarity : 0.004 0.061 3179 Dihedral : 6.202 117.529 2660 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer Outliers : 1.79 % 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: -0.97 (0.17), residues: 2361 helix: 0.55 (0.18), residues: 795 sheet: -0.58 (0.26), residues: 407 loop : -1.52 (0.18), residues: 1159 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 200 time to evaluate : 2.055 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 19 residues processed: 222 average time/residue: 0.3148 time to fit residues: 106.9186 Evaluate side-chains 206 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 187 time to evaluate : 2.108 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1848 time to fit residues: 9.3601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 0.6980 chunk 205 optimal weight: 4.9990 chunk 45 optimal weight: 9.9990 chunk 133 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 228 optimal weight: 0.0970 chunk 189 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 355 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 18448 Z= 0.200 Angle : 0.562 9.279 25153 Z= 0.286 Chirality : 0.041 0.245 2911 Planarity : 0.004 0.059 3179 Dihedral : 6.037 117.171 2660 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.29 % Favored : 92.71 % Rotamer Outliers : 1.29 % 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 (0.17), residues: 2361 helix: 0.70 (0.19), residues: 790 sheet: -0.57 (0.26), residues: 392 loop : -1.49 (0.18), residues: 1179 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 206 time to evaluate : 2.127 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 222 average time/residue: 0.3058 time to fit residues: 105.0148 Evaluate side-chains 201 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 2.092 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1738 time to fit residues: 6.1113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 192 optimal weight: 0.0670 chunk 127 optimal weight: 2.9990 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 overall best weight: 0.8122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 75 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6879 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 18448 Z= 0.233 Angle : 0.577 10.025 25153 Z= 0.290 Chirality : 0.042 0.218 2911 Planarity : 0.004 0.058 3179 Dihedral : 6.023 117.472 2660 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 1.06 % 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: -0.87 (0.17), residues: 2361 helix: 0.67 (0.19), residues: 794 sheet: -0.56 (0.26), residues: 402 loop : -1.48 (0.18), residues: 1165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 204 time to evaluate : 1.999 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 10 residues processed: 215 average time/residue: 0.3196 time to fit residues: 105.0053 Evaluate side-chains 201 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 191 time to evaluate : 2.000 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1678 time to fit residues: 5.8071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 3.9990 chunk 90 optimal weight: 0.6980 chunk 135 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 144 optimal weight: 8.9990 chunk 154 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 178 optimal weight: 9.9990 chunk 206 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6889 moved from start: 0.3819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 18448 Z= 0.246 Angle : 0.583 9.485 25153 Z= 0.296 Chirality : 0.042 0.213 2911 Planarity : 0.004 0.058 3179 Dihedral : 6.060 117.400 2660 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer Outliers : 0.45 % 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 (0.17), residues: 2361 helix: 0.73 (0.19), residues: 792 sheet: -0.58 (0.26), residues: 402 loop : -1.48 (0.18), residues: 1167 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 1.907 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 198 average time/residue: 0.3167 time to fit residues: 97.3140 Evaluate side-chains 199 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 193 time to evaluate : 2.045 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1697 time to fit residues: 4.6860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 211 optimal weight: 0.8980 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 65 optimal weight: 10.0000 chunk 191 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 139 optimal weight: 0.0270 chunk 224 optimal weight: 0.5980 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6894 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 18448 Z= 0.248 Angle : 0.593 9.524 25153 Z= 0.298 Chirality : 0.042 0.205 2911 Planarity : 0.004 0.058 3179 Dihedral : 6.062 117.280 2660 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer Outliers : 0.50 % 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: -0.87 (0.17), residues: 2361 helix: 0.71 (0.19), residues: 794 sheet: -0.58 (0.26), residues: 401 loop : -1.49 (0.18), residues: 1166 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 194 time to evaluate : 2.593 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 199 average time/residue: 0.3294 time to fit residues: 101.5654 Evaluate side-chains 197 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 192 time to evaluate : 2.026 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1716 time to fit residues: 4.1716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 235 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 187 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 114 optimal weight: 3.9990 chunk 148 optimal weight: 1.9990 chunk 199 optimal weight: 3.9990 overall best weight: 1.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 613 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.4194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 18448 Z= 0.352 Angle : 0.658 9.829 25153 Z= 0.333 Chirality : 0.045 0.214 2911 Planarity : 0.004 0.059 3179 Dihedral : 6.374 117.821 2660 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.39 % Favored : 91.61 % Rotamer Outliers : 0.17 % 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: -1.07 (0.17), residues: 2361 helix: 0.50 (0.18), residues: 800 sheet: -0.71 (0.26), residues: 404 loop : -1.59 (0.18), residues: 1157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4722 Ramachandran restraints generated. 2361 Oldfield, 0 Emsley, 2361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 198 time to evaluate : 2.056 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 199 average time/residue: 0.3096 time to fit residues: 95.6016 Evaluate side-chains 186 residues out of total 2017 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 185 time to evaluate : 1.946 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1569 time to fit residues: 2.8650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 4.9990 chunk 172 optimal weight: 0.9990 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 chunk 187 optimal weight: 0.6980 chunk 78 optimal weight: 4.9990 chunk 192 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 164 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 4 549 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.184049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.157606 restraints weight = 23678.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.154722 restraints weight = 41184.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.155693 restraints weight = 38706.840| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.4152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 18448 Z= 0.225 Angle : 0.606 10.290 25153 Z= 0.304 Chirality : 0.042 0.207 2911 Planarity : 0.004 0.059 3179 Dihedral : 6.131 116.873 2660 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.92 % Favored : 92.08 % Rotamer Outliers : 0.22 % 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: -0.92 (0.17), residues: 2361 helix: 0.69 (0.19), residues: 790 sheet: -0.62 (0.26), residues: 388 loop : -1.53 (0.18), residues: 1183 =============================================================================== Job complete usr+sys time: 3316.72 seconds wall clock time: 61 minutes 34.20 seconds (3694.20 seconds total)