Starting phenix.real_space_refine on Thu Mar 5 15:43:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm6_13522/03_2026/7pm6_13522.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm6_13522/03_2026/7pm6_13522.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm6_13522/03_2026/7pm6_13522.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm6_13522/03_2026/7pm6_13522.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm6_13522/03_2026/7pm6_13522.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm6_13522/03_2026/7pm6_13522.cif" } resolution = 3.0 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 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= 0.001 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 10 5.49 5 Mg 5 5.21 5 S 148 5.16 5 C 14835 2.51 5 N 3957 2.21 5 O 4379 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 105 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23334 Number of models: 1 Model: "" Number of chains: 18 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, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6092 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 27, 'TRANS': 718} Chain breaks: 4 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: "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, 'ASP:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 31 Chain: "D" Number of atoms: 6092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 746, 6092 Classifications: {'peptide': 746} Link IDs: {'PTRANS': 27, 'TRANS': 718} Chain breaks: 4 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: 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: "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: 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: "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: 5.67, per 1000 atoms: 0.24 Number of scatterers: 23334 At special positions: 0 Unit cell: (171.72, 224.72, 177.02, 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 10 15.00 Mg 5 11.99 O 4379 8.00 N 3957 7.00 C 14835 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: 2.16 Conformation dependent library (CDL) restraints added in 935.1 milliseconds 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 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: 5456 Finding SS restraints... Secondary structure from input PDB file: 151 helices and 35 sheets defined 54.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.213A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.472A 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 removed outlier: 3.572A pdb=" N SER B 150 " --> pdb=" O LYS B 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.628A pdb=" N LEU A 77 " --> pdb=" O LEU A 74 " (cutoff:3.500A) 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 removed outlier: 3.517A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.576A pdb=" N PHE A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 207 removed outlier: 3.526A 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 268 removed outlier: 4.203A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.522A pdb=" N LYS A 275 " --> pdb=" O PRO A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.205A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.959A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.869A 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 376 removed outlier: 3.909A pdb=" N CYS A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) 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: 3.682A 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: 3.773A 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 removed outlier: 3.920A pdb=" N LYS A 567 " --> pdb=" O GLY A 563 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.506A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 594 removed outlier: 3.598A pdb=" N GLU A 591 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLN A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 633 Processing helix chain 'A' and resid 635 through 653 removed outlier: 3.794A pdb=" N ALA A 653 " --> pdb=" O GLU A 649 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.586A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 697 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: 3.881A pdb=" N GLU A 733 " --> pdb=" O LYS A 729 " (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 'C' and resid 55 through 61 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.550A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.870A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.264A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET C 123 " --> pdb=" O MET C 119 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 removed outlier: 3.542A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR C 143 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.689A 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 181 through 194 Processing helix chain 'C' and resid 195 through 197 No H-bonds generated for 'chain 'C' and resid 195 through 197' Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.749A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.521A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 262 Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.677A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 337 through 349 removed outlier: 3.592A pdb=" N SER C 348 " --> pdb=" O SER C 344 " (cutoff:3.500A) Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.939A 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 373 removed outlier: 3.694A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 Processing helix chain 'E' and resid 29 through 39 removed outlier: 4.125A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.377A 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 'D' and resid 73 through 77 removed outlier: 3.685A pdb=" N LEU D 77 " --> pdb=" O LEU D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 116 through 119 removed outlier: 4.458A 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: 3.558A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 151 " --> pdb=" O TYR D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 184 removed outlier: 3.653A pdb=" N PHE D 180 " --> pdb=" O ALA D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 192 through 207 removed outlier: 3.576A 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 268 removed outlier: 4.141A pdb=" N TYR D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 275 Processing helix chain 'D' and resid 285 through 290 removed outlier: 4.244A pdb=" N GLN D 290 " --> pdb=" O HIS D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 removed outlier: 3.870A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 337 removed outlier: 3.916A 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 376 removed outlier: 3.814A pdb=" N CYS D 376 " --> pdb=" O ALA D 372 " (cutoff:3.500A) 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: 3.653A 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: 3.775A 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 removed outlier: 3.896A pdb=" N LYS D 567 " --> pdb=" O GLY D 563 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 582 removed outlier: 3.554A pdb=" N ILE D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 594 removed outlier: 3.561A pdb=" N GLU D 591 " --> pdb=" O LYS D 587 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N PHE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLN D 594 " --> pdb=" O PRO D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 629 through 633 Processing helix chain 'D' and resid 635 through 653 removed outlier: 3.664A pdb=" N ALA D 653 " --> pdb=" O GLU D 649 " (cutoff:3.500A) Processing helix chain 'D' and resid 674 through 685 removed outlier: 3.615A pdb=" N GLN D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 697 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: 3.987A pdb=" N GLU D 733 " --> pdb=" O LYS D 729 " (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 'F' and resid 55 through 62 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.550A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 removed outlier: 3.830A pdb=" N HIS F 101 " --> pdb=" O PRO F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.228A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET F 123 " --> pdb=" O MET F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 removed outlier: 3.519A pdb=" N SER F 141 " --> pdb=" O GLN F 137 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N TYR F 143 " --> pdb=" O VAL F 139 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.685A 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 181 through 194 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 removed outlier: 3.798A pdb=" N GLU F 207 " --> pdb=" O THR F 203 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 234 through 237 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.527A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.651A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 305 Processing helix chain 'F' and resid 308 through 319 Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'F' and resid 348 through 349 No H-bonds generated for 'chain 'F' and resid 348 through 349' Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.912A 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 373 removed outlier: 3.689A 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 removed outlier: 3.618A pdb=" N MET G 82 " --> pdb=" O ASN G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.816A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.212A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N MET G 123 " --> pdb=" O MET G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 145 removed outlier: 3.529A pdb=" N SER G 141 " --> pdb=" O GLN G 137 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR G 143 " --> pdb=" O VAL G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 removed outlier: 3.767A 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 181 through 194 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 removed outlier: 3.726A pdb=" N GLU G 207 " --> pdb=" O THR G 203 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VAL G 209 " --> pdb=" O GLU G 205 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASP G 211 " --> pdb=" O GLU G 207 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 252 through 257 removed outlier: 3.519A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 258 through 262 Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 283 Processing helix chain 'G' and resid 284 through 285 No H-bonds generated for 'chain 'G' and resid 284 through 285' Processing helix chain 'G' and resid 286 through 288 No H-bonds generated for 'chain 'G' and resid 286 through 288' Processing helix chain 'G' and resid 289 through 295 removed outlier: 3.781A pdb=" N ALA G 295 " --> pdb=" O LYS G 291 " (cutoff:3.500A) Processing helix chain 'G' and resid 301 through 305 Processing helix chain 'G' and resid 308 through 319 Processing helix chain 'G' and resid 337 through 349 removed outlier: 3.588A pdb=" N SER G 348 " --> pdb=" O SER G 344 " (cutoff:3.500A) Processing helix chain 'G' and resid 350 through 355 removed outlier: 3.983A 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 373 removed outlier: 3.838A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.544A pdb=" N LEU A 48 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 100 through 103 removed outlier: 6.419A pdb=" N GLN A 157 " --> pdb=" O GLY A 434 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N LEU A 436 " --> pdb=" O GLN A 157 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ILE A 159 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N ILE A 438 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 161 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.321A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 6.880A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.584A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.329A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (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: 6.334A 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 'E' and resid 26 through 28 Processing sheet with id=AB8, first strand: chain 'D' and resid 11 through 16 removed outlier: 3.753A pdb=" N ALA D 11 " --> pdb=" O LEU D 27 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 100 through 103 removed outlier: 6.466A pdb=" N GLN D 157 " --> pdb=" O GLY D 434 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU D 436 " --> pdb=" O GLN D 157 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE D 159 " --> pdb=" O LEU D 436 " (cutoff:3.500A) removed outlier: 7.653A pdb=" N ILE D 438 " --> pdb=" O ILE D 159 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N VAL D 161 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AC2, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.226A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 377 through 381 Processing sheet with id=AC4, first strand: chain 'D' and resid 538 through 539 Processing sheet with id=AC5, first strand: chain 'D' and resid 700 through 703 Processing sheet with id=AC6, first strand: chain 'F' and resid 29 through 32 removed outlier: 6.944A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (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: 6.374A 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: 6.811A pdb=" N LEU G 8 " --> pdb=" O LEU G 104 " (cutoff:3.500A) removed outlier: 8.605A pdb=" N THR G 106 " --> pdb=" O LEU G 8 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N CYS G 10 " --> pdb=" O THR G 106 " (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: 6.273A 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 1180 hydrogen bonds defined for protein. 3249 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.29 Time building geometry restraints manager: 2.86 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: 3891 1.31 - 1.44: 6319 1.44 - 1.56: 13364 1.56 - 1.69: 15 1.69 - 1.82: 242 Bond restraints: 23831 Sorted by residual: bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.432 0.140 2.00e-02 2.50e+03 4.87e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.435 0.137 2.00e-02 2.50e+03 4.69e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.469 0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" CA TRP J 1 " pdb=" C TRP J 1 " ideal model delta sigma weight residual 1.525 1.441 0.084 2.10e-02 2.27e+03 1.60e+01 bond pdb=" C EEP I 2 " pdb=" O EEP I 2 " ideal model delta sigma weight residual 1.263 1.189 0.074 2.00e-02 2.50e+03 1.38e+01 ... (remaining 23826 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.90: 31422 2.90 - 5.80: 706 5.80 - 8.70: 61 8.70 - 11.59: 22 11.59 - 14.49: 3 Bond angle restraints: 32214 Sorted by residual: angle pdb=" N TYR D 113 " pdb=" CA TYR D 113 " pdb=" CB TYR D 113 " ideal model delta sigma weight residual 113.15 103.69 9.46 1.63e+00 3.76e-01 3.37e+01 angle pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta sigma weight residual 121.70 111.40 10.30 1.80e+00 3.09e-01 3.27e+01 angle pdb=" N CYS I 5 " pdb=" CA CYS I 5 " pdb=" CB CYS I 5 " ideal model delta sigma weight residual 110.50 100.85 9.65 1.70e+00 3.46e-01 3.23e+01 angle pdb=" C HYP I 6 " pdb=" N ALA I 7 " pdb=" CA ALA I 7 " ideal model delta sigma weight residual 121.70 111.59 10.11 1.80e+00 3.09e-01 3.15e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 112.42 9.28 1.80e+00 3.09e-01 2.66e+01 ... (remaining 32209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.86: 13876 27.86 - 55.73: 410 55.73 - 83.59: 69 83.59 - 111.46: 12 111.46 - 139.32: 12 Dihedral angle restraints: 14379 sinusoidal: 5905 harmonic: 8474 Sorted by residual: dihedral pdb=" O1B ADP G 401 " pdb=" O3A ADP G 401 " pdb=" PB ADP G 401 " pdb=" PA ADP G 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.32 -139.32 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.28 -139.28 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 79.04 -139.04 1 2.00e+01 2.50e-03 4.21e+01 ... (remaining 14376 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2230 0.055 - 0.110: 1012 0.110 - 0.165: 237 0.165 - 0.219: 35 0.219 - 0.274: 12 Chirality restraints: 3526 Sorted by residual: chirality pdb=" CA DTH H 4 " pdb=" N DTH H 4 " pdb=" C DTH H 4 " pdb=" CB DTH H 4 " both_signs ideal model delta sigma weight residual False -2.53 -2.25 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CG LEU A 782 " pdb=" CB LEU A 782 " pdb=" CD1 LEU A 782 " pdb=" CD2 LEU A 782 " both_signs ideal model delta sigma weight residual False -2.59 -2.32 -0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA CYS I 5 " pdb=" N CYS I 5 " pdb=" C CYS I 5 " pdb=" CB CYS I 5 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 3523 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 113 " 0.057 2.00e-02 2.50e+03 4.60e-02 4.22e+01 pdb=" CG TYR D 113 " -0.106 2.00e-02 2.50e+03 pdb=" CD1 TYR D 113 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR D 113 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR D 113 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR D 113 " 0.023 2.00e-02 2.50e+03 pdb=" CZ TYR D 113 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR D 113 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 677 " 0.077 9.50e-02 1.11e+02 4.67e-02 1.30e+01 pdb=" NE ARG A 677 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 677 " 0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG A 677 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 677 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 677 " 0.079 9.50e-02 1.11e+02 4.69e-02 1.26e+01 pdb=" NE ARG D 677 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 677 " 0.059 2.00e-02 2.50e+03 pdb=" NH1 ARG D 677 " -0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG D 677 " -0.017 2.00e-02 2.50e+03 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.36: 38 2.36 - 2.99: 12842 2.99 - 3.63: 34361 3.63 - 4.26: 53661 4.26 - 4.90: 90888 Nonbonded interactions: 191790 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.724 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.727 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.731 3.620 nonbonded pdb="MG MG A1901 " pdb=" O1B ADP A1902 " model vdw 1.908 2.170 nonbonded pdb=" O2B ADP G 401 " pdb="MG MG G 402 " model vdw 1.968 2.170 ... (remaining 191785 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: 2.630 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: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 21.680 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:8.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 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 : 0.012 0.140 23837 Z= 0.521 Angle : 1.075 14.493 32232 Z= 0.595 Chirality : 0.063 0.274 3526 Planarity : 0.007 0.047 4109 Dihedral : 14.944 139.320 8905 Min Nonbonded Distance : 1.724 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 0.04 % Allowed : 0.52 % Favored : 99.44 % Cbeta Deviations : 0.15 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.14), residues: 2839 helix: -1.51 (0.12), residues: 1335 sheet: 0.01 (0.24), residues: 404 loop : 0.28 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.009 ARG A 677 TYR 0.106 0.006 TYR D 113 PHE 0.042 0.004 PHE D 564 TRP 0.046 0.005 TRP C 356 HIS 0.014 0.003 HIS A 260 Details of bonding type rmsd covalent geometry : bond 0.01219 (23831) covalent geometry : angle 1.07102 (32214) hydrogen bonds : bond 0.14481 ( 1174) hydrogen bonds : angle 6.91857 ( 3249) link_TRANS : bond 0.02174 ( 6) link_TRANS : angle 3.86711 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 266 time to evaluate : 0.802 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: C 355 MET cc_start: 0.8143 (mmm) cc_final: 0.7891 (mmt) REVERT: C 360 GLN cc_start: 0.8220 (tp40) cc_final: 0.7382 (tm-30) REVERT: E 120 MET cc_start: 0.4648 (mtm) cc_final: 0.4233 (mtt) REVERT: F 82 MET cc_start: 0.8444 (tpt) cc_final: 0.8142 (tpt) REVERT: G 360 GLN cc_start: 0.8238 (tp40) cc_final: 0.7949 (tp-100) outliers start: 1 outliers final: 3 residues processed: 267 average time/residue: 0.8652 time to fit residues: 255.6386 Evaluate side-chains 136 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 133 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 346 ASP 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 197 optimal weight: 0.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN A 214 ASN A 264 GLN A 410 ASN A 463 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 162 ASN C 280 ASN E 75 GLN D 214 ASN D 264 GLN D 395 HIS D 410 ASN D 418 HIS ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 162 ASN F 280 ASN G 280 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.086423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.056546 restraints weight = 93794.773| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 3.76 r_work: 0.2802 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23837 Z= 0.150 Angle : 0.688 10.929 32232 Z= 0.353 Chirality : 0.045 0.234 3526 Planarity : 0.004 0.042 4109 Dihedral : 10.529 138.839 3254 Min Nonbonded Distance : 1.925 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.61 % Allowed : 5.88 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.15), residues: 2839 helix: 0.39 (0.14), residues: 1362 sheet: 0.42 (0.24), residues: 421 loop : 0.86 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 95 TYR 0.044 0.002 TYR D 113 PHE 0.029 0.002 PHE C 255 TRP 0.015 0.002 TRP C 79 HIS 0.008 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00334 (23831) covalent geometry : angle 0.68810 (32214) hydrogen bonds : bond 0.04474 ( 1174) hydrogen bonds : angle 5.14047 ( 3249) link_TRANS : bond 0.00240 ( 6) link_TRANS : angle 0.76650 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 156 time to evaluate : 0.894 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: A 113 TYR cc_start: 0.8198 (OUTLIER) cc_final: 0.7918 (t80) REVERT: A 305 MET cc_start: 0.8559 (tmm) cc_final: 0.7895 (ppp) REVERT: A 346 ASP cc_start: 0.9161 (t70) cc_final: 0.8839 (t0) REVERT: A 364 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8459 (mpp) REVERT: A 507 ASP cc_start: 0.8533 (t0) cc_final: 0.8314 (t0) REVERT: C 176 MET cc_start: 0.8608 (OUTLIER) cc_final: 0.8284 (mpt) REVERT: C 269 MET cc_start: 0.8709 (mmm) cc_final: 0.8027 (ttm) REVERT: C 305 MET cc_start: 0.9341 (mmm) cc_final: 0.9109 (mmt) REVERT: C 355 MET cc_start: 0.9401 (mmm) cc_final: 0.9192 (mmt) REVERT: C 364 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8226 (mp0) REVERT: E 73 MET cc_start: 0.3846 (ptm) cc_final: 0.3567 (ptm) REVERT: D 715 MET cc_start: 0.3373 (OUTLIER) cc_final: 0.3091 (ptp) REVERT: G 47 MET cc_start: 0.8954 (mmm) cc_final: 0.7988 (ptm) REVERT: G 334 GLU cc_start: 0.8487 (pm20) cc_final: 0.8230 (pp20) outliers start: 40 outliers final: 7 residues processed: 181 average time/residue: 0.7141 time to fit residues: 146.5543 Evaluate side-chains 142 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 TYR Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 570 ASP Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 113 TYR Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 715 MET Chi-restraints excluded: chain G residue 257 CYS 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 84 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 228 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 231 optimal weight: 3.9990 chunk 179 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 166 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 207 optimal weight: 7.9990 chunk 142 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 395 HIS A 681 GLN A 730 ASN A 755 GLN ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.088801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.054302 restraints weight = 81011.782| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.27 r_work: 0.2747 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 23837 Z= 0.270 Angle : 0.701 11.911 32232 Z= 0.354 Chirality : 0.047 0.321 3526 Planarity : 0.004 0.041 4109 Dihedral : 9.703 147.379 3250 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.05 % Allowed : 7.66 % Favored : 90.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.16), residues: 2839 helix: 0.81 (0.14), residues: 1369 sheet: 0.68 (0.25), residues: 399 loop : 0.72 (0.20), residues: 1071 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 95 TYR 0.033 0.002 TYR D 113 PHE 0.016 0.002 PHE G 262 TRP 0.016 0.002 TRP A 781 HIS 0.007 0.001 HIS D 430 Details of bonding type rmsd covalent geometry : bond 0.00618 (23831) covalent geometry : angle 0.70105 (32214) hydrogen bonds : bond 0.04376 ( 1174) hydrogen bonds : angle 4.89068 ( 3249) link_TRANS : bond 0.00320 ( 6) link_TRANS : angle 0.68053 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 134 time to evaluate : 1.017 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: 0.8769 (tmm) cc_final: 0.8516 (ppp) REVERT: A 364 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8293 (mpp) REVERT: C 176 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8329 (mpt) REVERT: C 269 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.7942 (ttm) REVERT: C 355 MET cc_start: 0.9358 (mmm) cc_final: 0.9121 (mmt) REVERT: C 364 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8281 (mp0) REVERT: E 19 PHE cc_start: 0.5574 (m-80) cc_final: 0.5034 (m-80) REVERT: E 31 GLN cc_start: 0.7264 (tp-100) cc_final: 0.6904 (tp-100) REVERT: D 323 MET cc_start: 0.8759 (mmm) cc_final: 0.8510 (tpt) REVERT: D 364 MET cc_start: 0.9176 (mmm) cc_final: 0.8360 (mpp) REVERT: D 561 CYS cc_start: 0.8802 (m) cc_final: 0.8563 (p) REVERT: D 715 MET cc_start: 0.3551 (OUTLIER) cc_final: 0.3306 (ptp) REVERT: F 123 MET cc_start: 0.9175 (mmp) cc_final: 0.8926 (mmt) outliers start: 51 outliers final: 10 residues processed: 172 average time/residue: 0.6753 time to fit residues: 132.5569 Evaluate side-chains 139 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 385 GLU Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 269 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 715 MET Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 257 CYS 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 149 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 135 optimal weight: 10.0000 chunk 219 optimal weight: 0.9980 chunk 116 optimal weight: 0.9980 chunk 263 optimal weight: 3.9990 chunk 183 optimal weight: 2.9990 chunk 106 optimal weight: 0.2980 chunk 167 optimal weight: 0.9990 chunk 245 optimal weight: 0.9980 chunk 154 optimal weight: 20.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 12 ASN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 463 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.086719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.053845 restraints weight = 85596.078| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.03 r_work: 0.2806 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 23837 Z= 0.125 Angle : 0.603 11.265 32232 Z= 0.299 Chirality : 0.042 0.257 3526 Planarity : 0.004 0.046 4109 Dihedral : 9.164 149.102 3250 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.45 % Allowed : 9.51 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.16), residues: 2839 helix: 1.22 (0.14), residues: 1356 sheet: 0.83 (0.26), residues: 388 loop : 0.77 (0.20), residues: 1095 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 95 TYR 0.026 0.001 TYR A 787 PHE 0.017 0.001 PHE D 470 TRP 0.021 0.002 TRP A 702 HIS 0.005 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00285 (23831) covalent geometry : angle 0.60331 (32214) hydrogen bonds : bond 0.03589 ( 1174) hydrogen bonds : angle 4.62795 ( 3249) link_TRANS : bond 0.00141 ( 6) link_TRANS : angle 0.74896 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 141 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8762 (tmm) cc_final: 0.8517 (ppp) REVERT: A 346 ASP cc_start: 0.9236 (t70) cc_final: 0.8890 (t0) REVERT: A 364 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8365 (mpp) REVERT: A 749 ILE cc_start: 0.9357 (OUTLIER) cc_final: 0.9154 (tp) REVERT: C 176 MET cc_start: 0.8611 (OUTLIER) cc_final: 0.8286 (mpt) REVERT: C 269 MET cc_start: 0.8785 (mmm) cc_final: 0.8177 (ttm) REVERT: C 305 MET cc_start: 0.9373 (mmm) cc_final: 0.9093 (mmt) REVERT: C 355 MET cc_start: 0.9326 (mmm) cc_final: 0.9117 (mmm) REVERT: C 364 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8223 (mp0) REVERT: D 323 MET cc_start: 0.8677 (mmm) cc_final: 0.8352 (tpt) REVERT: D 364 MET cc_start: 0.9183 (mmm) cc_final: 0.8393 (mpp) REVERT: D 561 CYS cc_start: 0.8753 (m) cc_final: 0.8466 (p) REVERT: D 715 MET cc_start: 0.3070 (OUTLIER) cc_final: 0.2157 (ptp) REVERT: D 790 MET cc_start: 0.0397 (OUTLIER) cc_final: 0.0025 (ppp) REVERT: G 176 MET cc_start: 0.9004 (OUTLIER) cc_final: 0.8772 (mtt) outliers start: 36 outliers final: 8 residues processed: 164 average time/residue: 0.7590 time to fit residues: 140.6233 Evaluate side-chains 138 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain D residue 521 ASP Chi-restraints excluded: chain D residue 715 MET Chi-restraints excluded: chain D residue 790 MET Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 176 MET 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 76 optimal weight: 0.9990 chunk 192 optimal weight: 5.9990 chunk 133 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 0.0070 chunk 176 optimal weight: 0.9990 chunk 149 optimal weight: 0.9980 chunk 271 optimal weight: 4.9990 chunk 260 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 218 optimal weight: 2.9990 overall best weight: 1.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 680 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.087063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.054170 restraints weight = 84067.141| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 3.03 r_work: 0.2805 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 23837 Z= 0.141 Angle : 0.596 10.463 32232 Z= 0.295 Chirality : 0.043 0.284 3526 Planarity : 0.004 0.043 4109 Dihedral : 8.847 151.641 3250 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.14 % Allowed : 9.91 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.16), residues: 2839 helix: 1.38 (0.15), residues: 1347 sheet: 0.74 (0.26), residues: 393 loop : 0.70 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 779 TYR 0.023 0.001 TYR D 787 PHE 0.018 0.001 PHE E 67 TRP 0.019 0.002 TRP D 484 HIS 0.004 0.001 HIS F 275 Details of bonding type rmsd covalent geometry : bond 0.00324 (23831) covalent geometry : angle 0.59632 (32214) hydrogen bonds : bond 0.03520 ( 1174) hydrogen bonds : angle 4.53118 ( 3249) link_TRANS : bond 0.00132 ( 6) link_TRANS : angle 0.74902 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 129 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8345 (mpp) REVERT: A 749 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8977 (tp) REVERT: C 176 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8286 (mpt) REVERT: C 269 MET cc_start: 0.8812 (mmm) cc_final: 0.8311 (ttm) REVERT: C 276 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8447 (mt-10) REVERT: C 305 MET cc_start: 0.9371 (mmm) cc_final: 0.9102 (mmt) REVERT: C 355 MET cc_start: 0.9313 (mmm) cc_final: 0.9100 (mmm) REVERT: C 364 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8315 (mp0) REVERT: D 323 MET cc_start: 0.8680 (mmm) cc_final: 0.8302 (tpt) REVERT: D 364 MET cc_start: 0.9113 (mmm) cc_final: 0.8356 (mpp) REVERT: D 561 CYS cc_start: 0.8777 (m) cc_final: 0.8492 (p) REVERT: F 167 GLU cc_start: 0.8631 (mp0) cc_final: 0.8406 (mp0) REVERT: G 176 MET cc_start: 0.9017 (mtt) cc_final: 0.8804 (mtt) REVERT: G 180 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8839 (mp) REVERT: G 269 MET cc_start: 0.8946 (OUTLIER) cc_final: 0.8719 (mtm) REVERT: G 314 GLN cc_start: 0.9029 (OUTLIER) cc_final: 0.8643 (tt0) outliers start: 53 outliers final: 12 residues processed: 165 average time/residue: 0.7101 time to fit residues: 133.1276 Evaluate side-chains 146 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 580 LEU Chi-restraints excluded: chain A residue 676 LYS Chi-restraints excluded: chain A residue 702 TRP Chi-restraints excluded: chain A residue 749 ILE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 276 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 314 GLN 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 88 optimal weight: 9.9990 chunk 206 optimal weight: 20.0000 chunk 110 optimal weight: 4.9990 chunk 193 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 144 optimal weight: 1.9990 chunk 223 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 91 optimal weight: 0.0050 chunk 203 optimal weight: 10.0000 chunk 55 optimal weight: 0.0030 overall best weight: 0.7406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 418 HIS ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.092103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.057432 restraints weight = 78675.378| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.45 r_work: 0.2816 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.3474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23837 Z= 0.114 Angle : 0.588 10.300 32232 Z= 0.289 Chirality : 0.042 0.262 3526 Planarity : 0.004 0.042 4109 Dihedral : 8.621 149.196 3250 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.85 % Allowed : 10.96 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.53 (0.16), residues: 2839 helix: 1.50 (0.15), residues: 1347 sheet: 0.71 (0.26), residues: 393 loop : 0.71 (0.20), residues: 1099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 37 TYR 0.027 0.001 TYR A 787 PHE 0.016 0.001 PHE D 470 TRP 0.022 0.002 TRP A 781 HIS 0.005 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00261 (23831) covalent geometry : angle 0.58831 (32214) hydrogen bonds : bond 0.03322 ( 1174) hydrogen bonds : angle 4.46337 ( 3249) link_TRANS : bond 0.00134 ( 6) link_TRANS : angle 0.78062 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 130 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 MET cc_start: 0.8968 (OUTLIER) cc_final: 0.8393 (mpp) REVERT: A 371 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8966 (mmm) REVERT: A 715 MET cc_start: 0.3781 (mtt) cc_final: 0.3139 (mmt) REVERT: C 176 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8316 (mpt) REVERT: C 180 LEU cc_start: 0.9007 (mt) cc_final: 0.8734 (mm) REVERT: C 269 MET cc_start: 0.8792 (mmm) cc_final: 0.8584 (mtm) REVERT: C 364 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8270 (mp0) REVERT: D 323 MET cc_start: 0.8717 (mmm) cc_final: 0.8315 (tpt) REVERT: D 364 MET cc_start: 0.9147 (mmm) cc_final: 0.8418 (mpp) REVERT: D 561 CYS cc_start: 0.8767 (m) cc_final: 0.8473 (p) REVERT: F 167 GLU cc_start: 0.8666 (mp0) cc_final: 0.8410 (mp0) REVERT: F 211 ASP cc_start: 0.9000 (t0) cc_final: 0.8725 (t70) REVERT: G 269 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8763 (mtm) REVERT: G 314 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.8117 (tp-100) outliers start: 46 outliers final: 6 residues processed: 159 average time/residue: 0.7363 time to fit residues: 132.3224 Evaluate side-chains 136 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain G residue 64 ILE Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 269 MET Chi-restraints excluded: chain G residue 314 GLN 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 79 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 86 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 273 optimal weight: 0.7980 chunk 163 optimal weight: 10.0000 chunk 151 optimal weight: 7.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 31 GLN ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 730 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.081326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.046395 restraints weight = 88071.967| |-----------------------------------------------------------------------------| r_work (start): 0.2904 rms_B_bonded: 3.30 r_work: 0.2735 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 23837 Z= 0.295 Angle : 0.708 12.903 32232 Z= 0.349 Chirality : 0.046 0.269 3526 Planarity : 0.004 0.046 4109 Dihedral : 8.833 150.223 3250 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.57 % Allowed : 11.68 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.33 (0.16), residues: 2839 helix: 1.35 (0.14), residues: 1361 sheet: 0.64 (0.25), residues: 396 loop : 0.56 (0.20), residues: 1082 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 779 TYR 0.032 0.002 TYR D 10 PHE 0.017 0.002 PHE C 255 TRP 0.017 0.002 TRP I 1 HIS 0.011 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00676 (23831) covalent geometry : angle 0.70782 (32214) hydrogen bonds : bond 0.03988 ( 1174) hydrogen bonds : angle 4.71784 ( 3249) link_TRANS : bond 0.00368 ( 6) link_TRANS : angle 0.65711 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8703 (ppp) cc_final: 0.8217 (ppp) REVERT: A 364 MET cc_start: 0.8985 (OUTLIER) cc_final: 0.8339 (mpp) REVERT: C 176 MET cc_start: 0.8643 (OUTLIER) cc_final: 0.8333 (mpt) REVERT: C 269 MET cc_start: 0.8858 (mmm) cc_final: 0.8379 (ttm) REVERT: C 364 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8375 (mp0) REVERT: D 323 MET cc_start: 0.8749 (mmm) cc_final: 0.8305 (tpt) REVERT: D 364 MET cc_start: 0.9169 (mmm) cc_final: 0.8432 (mpp) REVERT: D 715 MET cc_start: 0.3251 (mpt) cc_final: 0.2976 (mmt) REVERT: F 167 GLU cc_start: 0.8668 (mp0) cc_final: 0.8352 (mp0) REVERT: G 47 MET cc_start: 0.8811 (mmm) cc_final: 0.8043 (ptm) outliers start: 39 outliers final: 10 residues processed: 152 average time/residue: 0.7241 time to fit residues: 124.8489 Evaluate side-chains 134 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 26 LYS Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain G residue 132 MET Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS 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 6 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 82 optimal weight: 30.0000 chunk 211 optimal weight: 0.4980 chunk 258 optimal weight: 0.9990 chunk 125 optimal weight: 10.0000 chunk 266 optimal weight: 0.7980 chunk 204 optimal weight: 9.9990 chunk 242 optimal weight: 0.8980 chunk 94 optimal weight: 0.8980 chunk 133 optimal weight: 20.0000 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 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN G 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.094235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.061441 restraints weight = 76116.730| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 4.49 r_work: 0.2760 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23837 Z= 0.121 Angle : 0.614 11.836 32232 Z= 0.300 Chirality : 0.042 0.254 3526 Planarity : 0.004 0.041 4109 Dihedral : 8.542 151.663 3250 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 0.85 % Allowed : 12.81 % Favored : 86.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.16), residues: 2839 helix: 1.56 (0.15), residues: 1345 sheet: 0.65 (0.25), residues: 413 loop : 0.61 (0.20), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 64 TYR 0.026 0.001 TYR A 787 PHE 0.016 0.001 PHE B 96 TRP 0.021 0.002 TRP A 781 HIS 0.005 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00277 (23831) covalent geometry : angle 0.61374 (32214) hydrogen bonds : bond 0.03343 ( 1174) hydrogen bonds : angle 4.48882 ( 3249) link_TRANS : bond 0.00164 ( 6) link_TRANS : angle 0.76163 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8747 (ppp) cc_final: 0.8279 (ppp) REVERT: A 364 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8362 (mpp) REVERT: A 715 MET cc_start: 0.3329 (mtt) cc_final: 0.2938 (mmt) REVERT: C 176 MET cc_start: 0.8672 (OUTLIER) cc_final: 0.8396 (mpt) REVERT: C 180 LEU cc_start: 0.9009 (mt) cc_final: 0.8617 (mp) REVERT: C 364 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8433 (mp0) REVERT: E 120 MET cc_start: 0.6424 (tpt) cc_final: 0.6128 (tpp) REVERT: D 323 MET cc_start: 0.8706 (mmm) cc_final: 0.8219 (tpt) REVERT: D 364 MET cc_start: 0.9140 (mmm) cc_final: 0.8430 (mpp) REVERT: D 715 MET cc_start: 0.3112 (mpt) cc_final: 0.2798 (mmt) REVERT: F 167 GLU cc_start: 0.8795 (mp0) cc_final: 0.8461 (mp0) REVERT: G 47 MET cc_start: 0.8778 (mmm) cc_final: 0.8145 (ptt) outliers start: 21 outliers final: 4 residues processed: 141 average time/residue: 0.7352 time to fit residues: 117.6681 Evaluate side-chains 129 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain G residue 257 CYS 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 248 optimal weight: 6.9990 chunk 74 optimal weight: 0.8980 chunk 143 optimal weight: 0.8980 chunk 209 optimal weight: 7.9990 chunk 221 optimal weight: 0.1980 chunk 259 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 223 optimal weight: 0.9990 chunk 224 optimal weight: 0.7980 chunk 178 optimal weight: 0.1980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 533 ASN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.087215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.054497 restraints weight = 85257.128| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.04 r_work: 0.2829 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 23837 Z= 0.109 Angle : 0.605 12.542 32232 Z= 0.294 Chirality : 0.042 0.304 3526 Planarity : 0.004 0.042 4109 Dihedral : 8.326 155.707 3250 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.77 % Allowed : 13.01 % Favored : 86.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.16), residues: 2839 helix: 1.63 (0.15), residues: 1351 sheet: 0.68 (0.25), residues: 413 loop : 0.64 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 64 TYR 0.027 0.001 TYR A 787 PHE 0.015 0.001 PHE D 470 TRP 0.024 0.002 TRP D 781 HIS 0.006 0.001 HIS D 418 Details of bonding type rmsd covalent geometry : bond 0.00247 (23831) covalent geometry : angle 0.60457 (32214) hydrogen bonds : bond 0.03183 ( 1174) hydrogen bonds : angle 4.38838 ( 3249) link_TRANS : bond 0.00168 ( 6) link_TRANS : angle 0.81382 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.018 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: 0.8785 (ppp) cc_final: 0.8273 (ppp) REVERT: A 364 MET cc_start: 0.8970 (mpp) cc_final: 0.8340 (mpp) REVERT: A 715 MET cc_start: 0.3864 (mtt) cc_final: 0.3422 (mmt) REVERT: C 176 MET cc_start: 0.8626 (OUTLIER) cc_final: 0.8279 (mpt) REVERT: C 364 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8300 (mp0) REVERT: E 120 MET cc_start: 0.6562 (tpt) cc_final: 0.6220 (tpp) REVERT: D 135 MET cc_start: 0.8451 (ttp) cc_final: 0.8177 (tmm) REVERT: D 323 MET cc_start: 0.8635 (mmm) cc_final: 0.8241 (tpt) REVERT: D 364 MET cc_start: 0.9068 (mmm) cc_final: 0.8422 (mpp) REVERT: D 715 MET cc_start: 0.3185 (mpt) cc_final: 0.2869 (mmt) REVERT: F 211 ASP cc_start: 0.8973 (t0) cc_final: 0.8647 (t70) REVERT: G 47 MET cc_start: 0.8748 (mmm) cc_final: 0.8171 (ptt) REVERT: G 314 GLN cc_start: 0.8983 (OUTLIER) cc_final: 0.8645 (tt0) outliers start: 19 outliers final: 4 residues processed: 143 average time/residue: 0.7530 time to fit residues: 121.8643 Evaluate side-chains 133 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 126 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 314 GLN 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 170 optimal weight: 1.9990 chunk 126 optimal weight: 40.0000 chunk 21 optimal weight: 10.0000 chunk 208 optimal weight: 6.9990 chunk 163 optimal weight: 9.9990 chunk 248 optimal weight: 6.9990 chunk 152 optimal weight: 7.9990 chunk 65 optimal weight: 0.3980 chunk 227 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 262 optimal weight: 4.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 373 HIS ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.082433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.047636 restraints weight = 88125.403| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 3.26 r_work: 0.2777 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 23837 Z= 0.179 Angle : 0.645 12.198 32232 Z= 0.314 Chirality : 0.043 0.296 3526 Planarity : 0.004 0.040 4109 Dihedral : 8.393 153.226 3250 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.32 % Allowed : 13.42 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.16), residues: 2839 helix: 1.65 (0.15), residues: 1347 sheet: 0.67 (0.25), residues: 413 loop : 0.65 (0.20), residues: 1079 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 64 TYR 0.029 0.001 TYR A 787 PHE 0.014 0.001 PHE C 255 TRP 0.019 0.002 TRP A 781 HIS 0.012 0.001 HIS A 424 Details of bonding type rmsd covalent geometry : bond 0.00412 (23831) covalent geometry : angle 0.64540 (32214) hydrogen bonds : bond 0.03463 ( 1174) hydrogen bonds : angle 4.47502 ( 3249) link_TRANS : bond 0.00194 ( 6) link_TRANS : angle 0.72141 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5678 Ramachandran restraints generated. 2839 Oldfield, 0 Emsley, 2839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 126 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.4771 (mmt) cc_final: 0.3223 (tpt) REVERT: A 203 MET cc_start: 0.8919 (mmp) cc_final: 0.8692 (mmp) REVERT: A 305 MET cc_start: 0.8857 (ppp) cc_final: 0.8391 (ppp) REVERT: A 364 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8308 (mpp) REVERT: C 176 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8357 (mpt) REVERT: E 120 MET cc_start: 0.6645 (tpt) cc_final: 0.6351 (tpp) REVERT: D 323 MET cc_start: 0.8755 (mmm) cc_final: 0.8297 (tpt) REVERT: D 364 MET cc_start: 0.9063 (mmm) cc_final: 0.8447 (mpp) REVERT: D 715 MET cc_start: 0.3423 (mpt) cc_final: 0.3104 (mmt) REVERT: F 167 GLU cc_start: 0.8697 (mp0) cc_final: 0.8368 (mp0) REVERT: F 211 ASP cc_start: 0.8985 (t0) cc_final: 0.8713 (t70) REVERT: G 47 MET cc_start: 0.8759 (mmm) cc_final: 0.8160 (ptt) REVERT: G 314 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.8670 (tt0) outliers start: 8 outliers final: 4 residues processed: 130 average time/residue: 0.7221 time to fit residues: 106.5477 Evaluate side-chains 129 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 122 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain C residue 176 MET Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain E residue 147 HIS Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain G residue 314 GLN 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 2 optimal weight: 30.0000 chunk 162 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 224 optimal weight: 0.9990 chunk 238 optimal weight: 0.9980 chunk 258 optimal weight: 0.7980 chunk 137 optimal weight: 0.0010 chunk 271 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 189 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 775 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 = 0.3923 r_free = 0.3923 target = 0.088504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.055272 restraints weight = 82966.980| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 3.13 r_work: 0.2829 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.4158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 23837 Z= 0.109 Angle : 0.620 12.922 32232 Z= 0.299 Chirality : 0.042 0.279 3526 Planarity : 0.003 0.042 4109 Dihedral : 8.206 156.494 3250 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.44 % Allowed : 13.54 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.61 (0.16), residues: 2839 helix: 1.66 (0.15), residues: 1351 sheet: 0.69 (0.26), residues: 413 loop : 0.63 (0.20), residues: 1075 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 37 TYR 0.029 0.001 TYR A 787 PHE 0.013 0.001 PHE D 470 TRP 0.025 0.002 TRP D 781 HIS 0.005 0.001 HIS D 138 Details of bonding type rmsd covalent geometry : bond 0.00248 (23831) covalent geometry : angle 0.61951 (32214) hydrogen bonds : bond 0.03177 ( 1174) hydrogen bonds : angle 4.40843 ( 3249) link_TRANS : bond 0.00162 ( 6) link_TRANS : angle 0.81272 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9752.13 seconds wall clock time: 166 minutes 11.78 seconds (9971.78 seconds total)