Starting phenix.real_space_refine on Sun Sep 29 23:14:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/09_2024/7pme_13530.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/09_2024/7pme_13530.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/09_2024/7pme_13530.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/09_2024/7pme_13530.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/09_2024/7pme_13530.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pme_13530/09_2024/7pme_13530.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 12 5.49 5 Mg 7 5.21 5 S 148 5.16 5 C 14851 2.51 5 N 3963 2.21 5 O 4389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 23370 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "C" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6105 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} Chain breaks: 5 Chain: "E" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "F" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2909 Classifications: {'peptide': 372} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 352} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Classifications: {'peptide': 3} Link IDs: {'TRANS': 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 26 Classifications: {'peptide': 4} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ANP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 14.63, per 1000 atoms: 0.63 Number of scatterers: 23370 At special positions: 0 Unit cell: (169.4, 209, 182.6, 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) S 148 16.00 P 12 15.00 Mg 7 11.99 O 4389 8.00 N 3963 7.00 C 14851 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " TRP H 1 " - " ALA H 7 " " DTH H 4 " - " ALA H 3 " " TRP I 1 " - " ALA I 7 " " DTH I 4 " - " ALA I 3 " " TRP J 1 " - " ALA J 7 " " DTH J 4 " - " ALA J 3 " Time building additional restraints: 6.11 Conformation dependent library (CDL) restraints added in 3.0 seconds 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH H 4 " pdb=" CB DTH I 4 " pdb=" CB DTH J 4 " Number of C-beta restraints generated: 5464 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 35 sheets defined 54.7% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.502A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.827A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 200 " --> pdb=" O VAL A 196 " (cutoff:3.500A) Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.146A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 271 No H-bonds generated for 'chain 'A' and resid 270 through 271' Processing helix chain 'A' and resid 272 through 278 removed outlier: 4.122A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 3.618A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.887A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.676A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 Processing helix chain 'A' and resid 483 through 487 removed outlier: 3.756A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 504 through 515 removed outlier: 3.767A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 532 Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.591A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 4.086A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 653 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.635A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 704 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 removed outlier: 3.515A pdb=" N THR A 727 " --> pdb=" O ASP A 723 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 734 " --> pdb=" O ASN A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.266A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 93 removed outlier: 3.501A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.118A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.610A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.660A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 183 through 196 removed outlier: 3.743A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 232 Processing helix chain 'C' and resid 252 through 260 Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 286 through 295 removed outlier: 3.729A pdb=" N ARG C 290 " --> pdb=" O ASP C 286 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 5.426A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.331A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.614A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.769A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.299A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 116 through 119 removed outlier: 4.421A pdb=" N TYR D 119 " --> pdb=" O LEU D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 116 through 119' Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.555A pdb=" N GLU D 145 " --> pdb=" O ALA D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 191 through 207 removed outlier: 3.774A pdb=" N LYS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN D 200 " --> pdb=" O VAL D 196 " (cutoff:3.500A) Proline residue: D 201 - end of helix Processing helix chain 'D' and resid 245 through 250 Processing helix chain 'D' and resid 259 through 269 removed outlier: 4.161A pdb=" N TYR D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 271 No H-bonds generated for 'chain 'D' and resid 270 through 271' Processing helix chain 'D' and resid 272 through 278 removed outlier: 4.065A pdb=" N THR D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 290 removed outlier: 3.667A pdb=" N GLN D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 removed outlier: 3.887A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 337 removed outlier: 3.646A pdb=" N ASN D 337 " --> pdb=" O LEU D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 365 Processing helix chain 'D' and resid 367 through 375 Processing helix chain 'D' and resid 392 through 424 Processing helix chain 'D' and resid 448 through 480 Processing helix chain 'D' and resid 483 through 487 removed outlier: 3.740A pdb=" N LEU D 486 " --> pdb=" O PRO D 483 " (cutoff:3.500A) Processing helix chain 'D' and resid 492 through 501 Processing helix chain 'D' and resid 504 through 515 removed outlier: 3.754A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 532 Processing helix chain 'D' and resid 563 through 569 Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.580A pdb=" N LEU D 580 " --> pdb=" O GLN D 576 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 594 removed outlier: 4.116A pdb=" N PHE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 635 through 653 Processing helix chain 'D' and resid 674 through 685 removed outlier: 3.655A pdb=" N GLN D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 Processing helix chain 'D' and resid 704 through 712 Processing helix chain 'D' and resid 713 through 715 No H-bonds generated for 'chain 'D' and resid 713 through 715' Processing helix chain 'D' and resid 723 through 736 removed outlier: 3.789A pdb=" N GLU D 733 " --> pdb=" O LYS D 729 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS D 734 " --> pdb=" O ASN D 730 " (cutoff:3.500A) Processing helix chain 'D' and resid 738 through 740 No H-bonds generated for 'chain 'D' and resid 738 through 740' Processing helix chain 'D' and resid 754 through 792 Processing helix chain 'E' and resid 5 through 19 Processing helix chain 'E' and resid 29 through 39 removed outlier: 4.155A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP E 34 " --> pdb=" O SER E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 Processing helix chain 'E' and resid 56 through 63 Processing helix chain 'E' and resid 67 through 79 Proline residue: E 72 - end of helix Processing helix chain 'E' and resid 87 through 95 Processing helix chain 'E' and resid 105 through 116 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'E' and resid 140 through 150 Processing helix chain 'F' and resid 55 through 61 Processing helix chain 'F' and resid 78 through 93 removed outlier: 3.513A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.117A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.647A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.637A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 183 through 194 removed outlier: 3.703A pdb=" N LYS F 191 " --> pdb=" O ASP F 187 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 232 Processing helix chain 'F' and resid 252 through 260 Proline residue: F 258 - end of helix Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 295 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.313A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 321 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 349 removed outlier: 3.604A pdb=" N SER F 348 " --> pdb=" O SER F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.770A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.344A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 Processing helix chain 'G' and resid 97 through 101 Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.163A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.599A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.644A pdb=" N ILE G 175 " --> pdb=" O PRO G 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 183 through 194 removed outlier: 3.697A pdb=" N LYS G 191 " --> pdb=" O ASP G 187 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 222 through 232 Processing helix chain 'G' and resid 252 through 260 Proline residue: G 258 - end of helix Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 286 through 295 removed outlier: 3.760A pdb=" N ARG G 290 " --> pdb=" O ASP G 286 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N LYS G 291 " --> pdb=" O ILE G 287 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASP G 292 " --> pdb=" O ASP G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.330A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 321 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.581A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.787A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 Processing helix chain 'G' and resid 368 through 374 removed outlier: 4.259A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.326A pdb=" N LEU A 107 " --> pdb=" O ARG A 660 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N ILE A 662 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA A 109 " --> pdb=" O ILE A 662 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N VAL A 659 " --> pdb=" O SER A 158 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE A 160 " --> pdb=" O VAL A 659 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N CYS A 661 " --> pdb=" O ILE A 160 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N SER A 162 " --> pdb=" O CYS A 661 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 211 removed outlier: 5.797A pdb=" N ALA A 209 " --> pdb=" O ASN A 216 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASN A 216 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.240A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 382 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA9, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.624A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 5.975A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 11 through 16 removed outlier: 4.096A pdb=" N ALA D 11 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 103 removed outlier: 6.331A pdb=" N LEU D 107 " --> pdb=" O ARG D 660 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N ILE D 662 " --> pdb=" O LEU D 107 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA D 109 " --> pdb=" O ILE D 662 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N VAL D 659 " --> pdb=" O SER D 158 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE D 160 " --> pdb=" O VAL D 659 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N CYS D 661 " --> pdb=" O ILE D 160 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N SER D 162 " --> pdb=" O CYS D 661 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLN D 157 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N LEU D 436 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ILE D 159 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE D 438 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N VAL D 161 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 211 removed outlier: 5.708A pdb=" N ALA D 209 " --> pdb=" O ASN D 216 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D 216 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.235A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 377 through 382 Processing sheet with id=AC3, first strand: chain 'D' and resid 538 through 539 Processing sheet with id=AC4, first strand: chain 'D' and resid 700 through 703 Processing sheet with id=AC5, first strand: chain 'E' and resid 26 through 28 Processing sheet with id=AC6, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.615A pdb=" N LYS F 18 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC8, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AD1, first strand: chain 'F' and resid 169 through 170 removed outlier: 5.991A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.600A pdb=" N LYS G 18 " --> pdb=" O ASP G 11 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.004A pdb=" N ASN G 297 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 238 through 241 1177 hydrogen bonds defined for protein. 3270 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: 8.97 Time building geometry restraints manager: 7.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3908 1.32 - 1.44: 6294 1.44 - 1.57: 13398 1.57 - 1.69: 20 1.69 - 1.81: 243 Bond restraints: 23863 Sorted by residual: bond pdb=" O3A ANP A1901 " pdb=" PB ANP A1901 " ideal model delta sigma weight residual 1.700 1.559 0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" O3A ANP D1901 " pdb=" PB ANP D1901 " ideal model delta sigma weight residual 1.700 1.561 0.139 2.00e-02 2.50e+03 4.84e+01 bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.73e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.450 0.122 2.00e-02 2.50e+03 3.71e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.454 0.118 2.00e-02 2.50e+03 3.50e+01 ... (remaining 23858 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.77: 32063 3.77 - 7.53: 165 7.53 - 11.30: 24 11.30 - 15.06: 2 15.06 - 18.83: 2 Bond angle restraints: 32256 Sorted by residual: angle pdb=" PB ANP A1901 " pdb=" N3B ANP A1901 " pdb=" PG ANP A1901 " ideal model delta sigma weight residual 126.95 108.12 18.83 3.00e+00 1.11e-01 3.94e+01 angle pdb=" PB ANP D1901 " pdb=" N3B ANP D1901 " pdb=" PG ANP D1901 " ideal model delta sigma weight residual 126.95 108.67 18.28 3.00e+00 1.11e-01 3.71e+01 angle pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta sigma weight residual 121.70 111.27 10.43 1.80e+00 3.09e-01 3.36e+01 angle pdb=" C HYP I 6 " pdb=" N ALA I 7 " pdb=" CA ALA I 7 " ideal model delta sigma weight residual 121.70 111.63 10.07 1.80e+00 3.09e-01 3.13e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 112.16 9.54 1.80e+00 3.09e-01 2.81e+01 ... (remaining 32251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.36: 13789 25.36 - 50.73: 484 50.73 - 76.09: 116 76.09 - 101.46: 43 101.46 - 126.82: 9 Dihedral angle restraints: 14441 sinusoidal: 5959 harmonic: 8482 Sorted by residual: dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.18 126.82 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" C5' ADP G 401 " pdb=" O5' ADP G 401 " pdb=" PA ADP G 401 " pdb=" O2A ADP G 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.24 126.76 1 2.00e+01 2.50e-03 3.84e+01 dihedral pdb=" C5' ADP F 401 " pdb=" O5' ADP F 401 " pdb=" PA ADP F 401 " pdb=" O2A ADP F 401 " ideal model delta sinusoidal sigma weight residual 300.00 173.27 126.74 1 2.00e+01 2.50e-03 3.84e+01 ... (remaining 14438 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2819 0.056 - 0.112: 601 0.112 - 0.168: 101 0.168 - 0.223: 7 0.223 - 0.279: 2 Chirality restraints: 3530 Sorted by residual: chirality pdb=" C3' ANP D1901 " pdb=" C2' ANP D1901 " pdb=" C4' ANP D1901 " pdb=" O3' ANP D1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' ANP A1901 " pdb=" C2' ANP A1901 " pdb=" C4' ANP A1901 " pdb=" O3' ANP A1901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.08e+00 ... (remaining 3527 not shown) Planarity restraints: 4117 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 231 " -0.262 9.50e-02 1.11e+02 1.21e-01 1.97e+01 pdb=" NE ARG D 231 " -0.004 2.00e-02 2.50e+03 pdb=" CZ ARG D 231 " 0.061 2.00e-02 2.50e+03 pdb=" NH1 ARG D 231 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG D 231 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 89 " -0.022 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C THR C 89 " 0.076 2.00e-02 2.50e+03 pdb=" O THR C 89 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE C 90 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR F 89 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C THR F 89 " 0.076 2.00e-02 2.50e+03 pdb=" O THR F 89 " -0.028 2.00e-02 2.50e+03 pdb=" N PHE F 90 " -0.026 2.00e-02 2.50e+03 ... (remaining 4114 not shown) Histogram of nonbonded interaction distances: 1.37 - 2.08: 8 2.08 - 2.78: 5041 2.78 - 3.49: 31786 3.49 - 4.19: 55047 4.19 - 4.90: 99088 Nonbonded interactions: 190970 Sorted by model distance: nonbonded pdb=" OE2 GLU C 205 " pdb=" CG2 DTH I 4 " model vdw 1.375 3.460 nonbonded pdb=" CG2 DTH H 4 " pdb=" OE2 GLU G 205 " model vdw 1.375 3.460 nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.731 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.732 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.733 3.620 ... (remaining 190965 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.460 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: 0.020 Extract box with map and model: 1.020 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 53.800 Find NCS groups from input model: 0.790 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 0.141 23863 Z= 0.314 Angle : 0.826 18.831 32256 Z= 0.466 Chirality : 0.048 0.279 3530 Planarity : 0.007 0.121 4111 Dihedral : 15.513 126.822 8959 Min Nonbonded Distance : 1.375 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.08 % Allowed : 0.04 % Favored : 99.88 % Cbeta Deviations : 0.11 % 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: -1.26 (0.14), residues: 2837 helix: -1.75 (0.11), residues: 1340 sheet: 0.29 (0.25), residues: 384 loop : 0.32 (0.17), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP F 340 HIS 0.005 0.001 HIS G 101 PHE 0.050 0.002 PHE A 564 TYR 0.029 0.005 TYR G 306 ARG 0.058 0.011 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 233 time to evaluate : 2.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 MET cc_start: 0.8216 (mmm) cc_final: 0.8014 (mmm) REVERT: B 27 ILE cc_start: 0.5414 (pt) cc_final: 0.4910 (pt) REVERT: D 150 MET cc_start: 0.8567 (ttp) cc_final: 0.8349 (ttm) REVERT: D 783 MET cc_start: 0.7751 (mmm) cc_final: 0.7404 (mmp) REVERT: E 12 PHE cc_start: 0.6453 (m-10) cc_final: 0.5808 (m-80) REVERT: E 29 TYR cc_start: 0.6369 (m-80) cc_final: 0.6108 (m-80) REVERT: E 89 TYR cc_start: 0.6834 (m-80) cc_final: 0.6556 (m-80) REVERT: F 305 MET cc_start: 0.8619 (mmm) cc_final: 0.8244 (mmt) outliers start: 2 outliers final: 3 residues processed: 235 average time/residue: 1.7084 time to fit residues: 448.8208 Evaluate side-chains 129 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 126 time to evaluate : 2.725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 240 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 145 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 135 optimal weight: 0.7980 chunk 166 optimal weight: 5.9990 chunk 258 optimal weight: 0.8980 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 354 HIS A 398 ASN A 493 GLN A 642 ASN A 775 GLN B 75 GLN C 162 ASN C 280 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 264 GLN D 398 ASN D 493 GLN D 775 GLN E 75 GLN F 162 ASN F 280 ASN G 162 ASN G 280 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23863 Z= 0.275 Angle : 0.658 7.897 32256 Z= 0.341 Chirality : 0.044 0.207 3530 Planarity : 0.004 0.043 4111 Dihedral : 10.805 129.412 3295 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 1.33 % Allowed : 4.42 % Favored : 94.25 % 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: 0.83 (0.15), residues: 2837 helix: 0.59 (0.13), residues: 1380 sheet: 0.60 (0.26), residues: 379 loop : 0.78 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP A 484 HIS 0.005 0.001 HIS A 81 PHE 0.025 0.001 PHE A 564 TYR 0.017 0.001 TYR F 294 ARG 0.010 0.001 ARG D 343 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 134 time to evaluate : 2.919 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8224 (tpp) REVERT: D 150 MET cc_start: 0.8568 (ttp) cc_final: 0.8362 (ttm) REVERT: D 783 MET cc_start: 0.7713 (mmm) cc_final: 0.7420 (mmt) REVERT: E 89 TYR cc_start: 0.6985 (m-80) cc_final: 0.6685 (m-80) REVERT: F 299 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7891 (mtm) REVERT: F 305 MET cc_start: 0.8614 (mmm) cc_final: 0.8386 (mmt) outliers start: 33 outliers final: 11 residues processed: 145 average time/residue: 1.5210 time to fit residues: 251.3349 Evaluate side-chains 128 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 115 time to evaluate : 2.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 467 MET Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 143 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 215 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 71 optimal weight: 9.9990 chunk 259 optimal weight: 0.9980 chunk 280 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 257 optimal weight: 0.7980 chunk 88 optimal weight: 5.9990 chunk 208 optimal weight: 30.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 23863 Z= 0.209 Angle : 0.586 7.922 32256 Z= 0.297 Chirality : 0.042 0.192 3530 Planarity : 0.004 0.051 4111 Dihedral : 9.852 133.416 3294 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 1.13 % Allowed : 5.67 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.16), residues: 2837 helix: 1.36 (0.14), residues: 1377 sheet: 0.75 (0.27), residues: 391 loop : 0.71 (0.19), residues: 1069 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP G 79 HIS 0.005 0.001 HIS A 81 PHE 0.023 0.001 PHE E 12 TYR 0.011 0.001 TYR F 166 ARG 0.009 0.000 ARG D 231 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 121 time to evaluate : 2.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8196 (tpp) REVERT: B 105 MET cc_start: 0.8012 (mpm) cc_final: 0.7697 (mpp) REVERT: D 150 MET cc_start: 0.8609 (ttp) cc_final: 0.8286 (ttm) REVERT: D 783 MET cc_start: 0.7718 (mmm) cc_final: 0.7400 (mmp) REVERT: D 790 MET cc_start: 0.3909 (ppp) cc_final: 0.3544 (pp-130) REVERT: E 89 TYR cc_start: 0.6980 (m-80) cc_final: 0.6564 (m-80) REVERT: F 47 MET cc_start: 0.7997 (mmm) cc_final: 0.7797 (mmm) REVERT: F 299 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.7948 (mtm) REVERT: G 299 MET cc_start: 0.7987 (mmm) cc_final: 0.7726 (mtt) outliers start: 28 outliers final: 11 residues processed: 133 average time/residue: 1.4451 time to fit residues: 220.6356 Evaluate side-chains 124 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 2.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 305 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 256 optimal weight: 1.9990 chunk 194 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 123 optimal weight: 0.8980 chunk 174 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 275 optimal weight: 1.9990 chunk 135 optimal weight: 0.9990 chunk 246 optimal weight: 5.9990 chunk 74 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 23863 Z= 0.189 Angle : 0.553 8.543 32256 Z= 0.278 Chirality : 0.041 0.193 3530 Planarity : 0.004 0.037 4111 Dihedral : 9.260 135.491 3292 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.84 % Allowed : 7.48 % Favored : 91.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.16), residues: 2837 helix: 1.67 (0.14), residues: 1377 sheet: 0.73 (0.28), residues: 371 loop : 0.72 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP G 79 HIS 0.005 0.001 HIS A 81 PHE 0.049 0.001 PHE E 12 TYR 0.010 0.001 TYR A 742 ARG 0.006 0.000 ARG A 231 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 2.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 150 MET cc_start: 0.8596 (ttp) cc_final: 0.8292 (ttm) REVERT: D 648 MET cc_start: 0.8841 (mmm) cc_final: 0.8632 (mmm) REVERT: D 783 MET cc_start: 0.7707 (mmm) cc_final: 0.7381 (mmp) REVERT: D 790 MET cc_start: 0.3685 (ppp) cc_final: 0.3249 (pp-130) REVERT: E 89 TYR cc_start: 0.6977 (m-80) cc_final: 0.6575 (m-80) REVERT: F 47 MET cc_start: 0.7986 (mmm) cc_final: 0.7765 (mmm) REVERT: F 299 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7980 (mtm) REVERT: G 299 MET cc_start: 0.7963 (mmm) cc_final: 0.7757 (mtt) outliers start: 21 outliers final: 9 residues processed: 125 average time/residue: 1.4244 time to fit residues: 204.9431 Evaluate side-chains 119 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 2.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 229 optimal weight: 3.9990 chunk 156 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 205 optimal weight: 40.0000 chunk 113 optimal weight: 3.9990 chunk 235 optimal weight: 6.9990 chunk 190 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 247 optimal weight: 1.9990 chunk 69 optimal weight: 9.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 354 HIS D 377 HIS ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.091 23863 Z= 0.571 Angle : 0.716 9.706 32256 Z= 0.363 Chirality : 0.047 0.205 3530 Planarity : 0.004 0.042 4111 Dihedral : 9.388 139.313 3292 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.05 % Allowed : 8.29 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.16), residues: 2837 helix: 1.39 (0.14), residues: 1388 sheet: 0.60 (0.27), residues: 391 loop : 0.40 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP G 79 HIS 0.006 0.001 HIS A 418 PHE 0.049 0.002 PHE E 12 TYR 0.018 0.002 TYR A 259 ARG 0.005 0.001 ARG A 542 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 2.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8688 (tpp) cc_final: 0.8317 (tpp) REVERT: C 132 MET cc_start: 0.8116 (ppp) cc_final: 0.7847 (ptp) REVERT: D 150 MET cc_start: 0.8677 (ttp) cc_final: 0.8431 (ttm) REVERT: D 783 MET cc_start: 0.7794 (mmm) cc_final: 0.7476 (mmp) REVERT: F 299 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7925 (mtm) outliers start: 26 outliers final: 12 residues processed: 127 average time/residue: 1.4731 time to fit residues: 214.5971 Evaluate side-chains 121 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 2.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 92 optimal weight: 0.0980 chunk 248 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 68 optimal weight: 9.9990 chunk 275 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 127 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 91 optimal weight: 0.0970 chunk 144 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 642 ASN ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 410 ASN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 23863 Z= 0.160 Angle : 0.555 9.553 32256 Z= 0.278 Chirality : 0.041 0.182 3530 Planarity : 0.003 0.044 4111 Dihedral : 9.039 145.994 3292 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Rotamer: Outliers : 0.72 % Allowed : 9.05 % Favored : 90.23 % 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: 1.69 (0.16), residues: 2837 helix: 1.82 (0.14), residues: 1377 sheet: 0.76 (0.27), residues: 386 loop : 0.46 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 781 HIS 0.007 0.001 HIS E 111 PHE 0.046 0.001 PHE E 12 TYR 0.009 0.001 TYR A 79 ARG 0.019 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 2.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8559 (tpp) cc_final: 0.8117 (tpp) REVERT: C 132 MET cc_start: 0.8070 (ppp) cc_final: 0.7763 (ptp) REVERT: D 150 MET cc_start: 0.8619 (ttp) cc_final: 0.8369 (ttm) REVERT: D 783 MET cc_start: 0.7728 (mmm) cc_final: 0.7422 (mmp) REVERT: F 299 MET cc_start: 0.8348 (OUTLIER) cc_final: 0.7965 (mtm) REVERT: G 299 MET cc_start: 0.7865 (mmm) cc_final: 0.7582 (mtt) outliers start: 18 outliers final: 11 residues processed: 129 average time/residue: 1.4545 time to fit residues: 215.7141 Evaluate side-chains 122 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 2.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 265 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 157 optimal weight: 0.9980 chunk 201 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 232 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 274 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 126 optimal weight: 8.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23863 Z= 0.205 Angle : 0.572 10.739 32256 Z= 0.282 Chirality : 0.041 0.185 3530 Planarity : 0.003 0.039 4111 Dihedral : 8.890 144.403 3292 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 0.60 % Allowed : 9.98 % Favored : 89.42 % 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: 1.74 (0.16), residues: 2837 helix: 1.89 (0.14), residues: 1377 sheet: 0.74 (0.27), residues: 386 loop : 0.47 (0.19), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 781 HIS 0.010 0.001 HIS B 111 PHE 0.048 0.001 PHE E 12 TYR 0.009 0.001 TYR A 456 ARG 0.012 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 3.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8569 (tpp) cc_final: 0.8211 (tpp) REVERT: D 150 MET cc_start: 0.8645 (ttp) cc_final: 0.8376 (ttm) REVERT: D 783 MET cc_start: 0.7753 (mmm) cc_final: 0.7424 (mmp) REVERT: D 788 MET cc_start: 0.7196 (tpt) cc_final: 0.6692 (mtt) REVERT: F 299 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7986 (mtm) REVERT: G 299 MET cc_start: 0.7802 (mmm) cc_final: 0.7532 (mtt) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 1.5091 time to fit residues: 218.1628 Evaluate side-chains 122 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 2.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 169 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 164 optimal weight: 3.9990 chunk 82 optimal weight: 30.0000 chunk 53 optimal weight: 0.7980 chunk 174 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 135 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 249 optimal weight: 6.9990 overall best weight: 2.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 23863 Z= 0.295 Angle : 0.609 11.855 32256 Z= 0.300 Chirality : 0.042 0.188 3530 Planarity : 0.004 0.039 4111 Dihedral : 8.854 144.146 3292 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.88 % Allowed : 9.77 % Favored : 89.34 % 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: 1.72 (0.16), residues: 2837 helix: 1.87 (0.14), residues: 1373 sheet: 0.75 (0.26), residues: 406 loop : 0.46 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 781 HIS 0.014 0.001 HIS B 111 PHE 0.060 0.001 PHE B 12 TYR 0.012 0.001 TYR A 259 ARG 0.011 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 2.958 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8565 (tpp) cc_final: 0.8170 (tpp) REVERT: C 132 MET cc_start: 0.8115 (ppp) cc_final: 0.7798 (ptp) REVERT: D 150 MET cc_start: 0.8642 (ttp) cc_final: 0.8379 (ttm) REVERT: D 439 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8580 (p90) REVERT: D 783 MET cc_start: 0.7834 (mmm) cc_final: 0.7513 (mmp) REVERT: F 299 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.8004 (mtm) REVERT: G 299 MET cc_start: 0.7808 (mmm) cc_final: 0.7544 (mtt) outliers start: 22 outliers final: 14 residues processed: 126 average time/residue: 1.4251 time to fit residues: 206.7585 Evaluate side-chains 125 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 109 time to evaluate : 2.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 239 MET Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain G residue 323 SER Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 263 optimal weight: 8.9990 chunk 240 optimal weight: 4.9990 chunk 255 optimal weight: 0.7980 chunk 154 optimal weight: 0.0270 chunk 111 optimal weight: 0.9980 chunk 201 optimal weight: 40.0000 chunk 78 optimal weight: 7.9990 chunk 231 optimal weight: 0.7980 chunk 242 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 270 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 111 ASN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 157 GLN ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23863 Z= 0.147 Angle : 0.594 14.707 32256 Z= 0.288 Chirality : 0.041 0.181 3530 Planarity : 0.003 0.039 4111 Dihedral : 8.659 144.569 3292 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.60 % Allowed : 10.26 % Favored : 89.14 % 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: 1.78 (0.16), residues: 2837 helix: 1.95 (0.14), residues: 1377 sheet: 0.72 (0.27), residues: 390 loop : 0.46 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 781 HIS 0.016 0.001 HIS B 111 PHE 0.058 0.001 PHE B 12 TYR 0.009 0.001 TYR A 79 ARG 0.011 0.000 ARG B 110 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 2.573 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 150 MET cc_start: 0.8639 (ttp) cc_final: 0.8375 (ttm) REVERT: D 783 MET cc_start: 0.7800 (mmm) cc_final: 0.7497 (mmp) REVERT: D 788 MET cc_start: 0.7348 (tpt) cc_final: 0.6982 (mtt) REVERT: F 299 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.7961 (mtm) REVERT: G 299 MET cc_start: 0.7870 (mmm) cc_final: 0.7635 (mtt) outliers start: 15 outliers final: 11 residues processed: 126 average time/residue: 1.4538 time to fit residues: 211.3565 Evaluate side-chains 124 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 112 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 165 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 188 optimal weight: 6.9990 chunk 283 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 226 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 174 optimal weight: 0.5980 chunk 138 optimal weight: 0.9990 chunk 179 optimal weight: 1.9990 chunk 240 optimal weight: 5.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 137 GLN ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 23863 Z= 0.201 Angle : 0.618 16.591 32256 Z= 0.299 Chirality : 0.041 0.210 3530 Planarity : 0.003 0.040 4111 Dihedral : 8.573 140.717 3292 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.44 % Allowed : 10.70 % Favored : 88.86 % 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: 1.79 (0.16), residues: 2837 helix: 1.96 (0.14), residues: 1377 sheet: 0.73 (0.27), residues: 390 loop : 0.48 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 781 HIS 0.016 0.001 HIS B 111 PHE 0.058 0.001 PHE B 12 TYR 0.009 0.001 TYR A 259 ARG 0.010 0.000 ARG B 110 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5674 Ramachandran restraints generated. 2837 Oldfield, 0 Emsley, 2837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 111 time to evaluate : 2.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 790 MET cc_start: -0.1344 (ttm) cc_final: -0.2111 (ppp) REVERT: C 132 MET cc_start: 0.8158 (ppp) cc_final: 0.7773 (ptp) REVERT: D 150 MET cc_start: 0.8651 (ttp) cc_final: 0.8383 (ttm) REVERT: D 783 MET cc_start: 0.7789 (mmm) cc_final: 0.7506 (mmp) REVERT: D 788 MET cc_start: 0.7344 (tpt) cc_final: 0.7046 (mmt) REVERT: E 120 MET cc_start: 0.0718 (mmm) cc_final: 0.0481 (tpt) REVERT: F 299 MET cc_start: 0.8324 (OUTLIER) cc_final: 0.7998 (mtm) REVERT: G 299 MET cc_start: 0.7860 (mmm) cc_final: 0.7570 (mtt) outliers start: 11 outliers final: 11 residues processed: 119 average time/residue: 1.5018 time to fit residues: 205.1283 Evaluate side-chains 122 residues out of total 2508 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 110 time to evaluate : 2.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 691 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain D residue 384 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain F residue 286 ASP Chi-restraints excluded: chain F residue 299 MET Chi-restraints excluded: chain I residue 5 CYS Chi-restraints excluded: chain G residue 80 ASP Chi-restraints excluded: chain G residue 151 ILE Chi-restraints excluded: chain J residue 5 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 69 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 226 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 232 optimal weight: 4.9990 chunk 28 optimal weight: 6.9990 chunk 41 optimal weight: 0.1980 chunk 198 optimal weight: 0.4980 chunk 12 optimal weight: 0.0980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 681 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.058226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.038481 restraints weight = 105532.438| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 3.63 r_work: 0.2728 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23863 Z= 0.223 Angle : 0.623 14.396 32256 Z= 0.301 Chirality : 0.042 0.208 3530 Planarity : 0.003 0.040 4111 Dihedral : 8.519 138.358 3292 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.40 % Allowed : 10.74 % Favored : 88.86 % 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: 1.79 (0.16), residues: 2837 helix: 1.96 (0.14), residues: 1377 sheet: 0.74 (0.27), residues: 390 loop : 0.47 (0.19), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 781 HIS 0.016 0.001 HIS B 111 PHE 0.057 0.001 PHE B 12 TYR 0.010 0.001 TYR A 259 ARG 0.010 0.000 ARG B 110 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6131.42 seconds wall clock time: 109 minutes 42.69 seconds (6582.69 seconds total)