Starting phenix.real_space_refine on Thu Mar 5 15:37:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7plu_13502/03_2026/7plu_13502.cif Found real_map, /net/cci-nas-00/data/ceres_data/7plu_13502/03_2026/7plu_13502.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7plu_13502/03_2026/7plu_13502.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7plu_13502/03_2026/7plu_13502.map" model { file = "/net/cci-nas-00/data/ceres_data/7plu_13502/03_2026/7plu_13502.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7plu_13502/03_2026/7plu_13502.cif" } resolution = 3.2 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 148 5.16 5 C 14821 2.51 5 N 3949 2.21 5 O 4361 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 90 residue(s): 0.02s 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: 23288 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} 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: "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: "D" Number of atoms: 6097 Number of conformers: 1 Conformer: "" Number of residues, atoms: 747, 6097 Classifications: {'peptide': 747} Link IDs: {'PTRANS': 27, 'TRANS': 719} 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: "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: "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: "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: "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: 5.26, per 1000 atoms: 0.23 Number of scatterers: 23288 At special positions: 0 Unit cell: (169.6, 208.82, 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 6 15.00 Mg 3 11.99 O 4361 8.00 N 3949 7.00 C 14821 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: 2.06 Conformation dependent library (CDL) restraints added in 927.6 milliseconds 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 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: 5460 Finding SS restraints... Secondary structure from input PDB file: 155 helices and 35 sheets defined 55.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.155A 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 131 through 135 removed outlier: 3.656A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.534A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 151 " --> pdb=" O TYR A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 removed outlier: 3.624A pdb=" N LYS A 195 " --> pdb=" O ASN A 191 " (cutoff:3.500A) removed outlier: 3.751A 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: 4.238A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 278 removed outlier: 4.608A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 292 removed outlier: 4.091A pdb=" N GLY A 291 " --> pdb=" O THR A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 4.156A pdb=" N VAL A 306 " --> pdb=" O ALA A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.584A 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: 4.043A 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: 3.534A pdb=" N LEU A 486 " --> pdb=" O PRO A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 500 removed outlier: 3.547A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ILE A 499 " --> pdb=" O CYS A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 515 removed outlier: 3.721A 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 564 through 569 removed outlier: 3.510A pdb=" N LYS A 569 " --> pdb=" O LEU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.677A pdb=" N ILE A 577 " --> pdb=" O TYR A 573 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER A 582 " --> pdb=" O LYS A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.044A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.733A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.567A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) 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 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: 3.594A pdb=" N LYS C 84 " --> pdb=" O ASP C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.306A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 146 removed outlier: 3.841A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 194 removed outlier: 3.757A pdb=" N THR C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) 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: 4.324A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP C 211 " --> pdb=" O GLU C 207 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLU C 214 " --> pdb=" O ARG C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.667A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 237 Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.718A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) Proline residue: C 258 - end of helix No H-bonds generated for 'chain 'C' and resid 252 through 260' Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 removed outlier: 3.534A pdb=" N CYS C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 296 Processing helix chain 'C' and resid 301 through 306 removed outlier: 4.384A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 348 through 355 removed outlier: 6.026A pdb=" N THR C 351 " --> pdb=" O SER C 348 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.725A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 374 removed outlier: 3.864A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 20 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.105A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 106 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 141 through 150 Processing helix chain 'D' and resid 73 through 77 Processing helix chain 'D' and resid 81 through 95 Processing helix chain 'D' and resid 116 through 119 removed outlier: 4.112A 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 131 through 135 removed outlier: 3.695A pdb=" N MET D 135 " --> pdb=" O MET D 132 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 153 removed outlier: 3.538A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 167 Processing helix chain 'D' and resid 168 through 185 Processing helix chain 'D' and resid 191 through 207 removed outlier: 3.811A pdb=" N LYS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 3.727A 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: 4.217A pdb=" N TYR D 263 " --> pdb=" O TYR D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 278 removed outlier: 4.579A pdb=" N THR D 276 " --> pdb=" O GLU D 273 " (cutoff:3.500A) Processing helix chain 'D' and resid 288 through 292 removed outlier: 4.058A pdb=" N GLY D 291 " --> pdb=" O THR D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 300 through 315 removed outlier: 4.073A pdb=" N VAL D 306 " --> pdb=" O ALA D 302 " (cutoff:3.500A) Processing helix chain 'D' and resid 318 through 337 removed outlier: 3.627A 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: 3.999A 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 Processing helix chain 'D' and resid 492 through 500 removed outlier: 3.591A pdb=" N LEU D 498 " --> pdb=" O PRO D 494 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 499 " --> pdb=" O CYS D 495 " (cutoff:3.500A) Processing helix chain 'D' and resid 506 through 515 removed outlier: 3.792A pdb=" N LYS D 514 " --> pdb=" O ASP D 510 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N MET D 515 " --> pdb=" O GLU D 511 " (cutoff:3.500A) Processing helix chain 'D' and resid 519 through 532 Processing helix chain 'D' and resid 564 through 569 removed outlier: 3.509A pdb=" N LYS D 569 " --> pdb=" O LEU D 565 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.607A pdb=" N ILE D 577 " --> pdb=" O TYR D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 587 through 593 removed outlier: 4.052A pdb=" N PHE D 593 " --> pdb=" O LEU D 589 " (cutoff:3.500A) Processing helix chain 'D' and resid 630 through 634 Processing helix chain 'D' and resid 635 through 652 Processing helix chain 'D' and resid 674 through 685 removed outlier: 3.779A pdb=" N GLN D 680 " --> pdb=" O LYS D 676 " (cutoff:3.500A) Processing helix chain 'D' and resid 686 through 696 removed outlier: 3.736A pdb=" N ALA D 696 " --> pdb=" O ARG D 692 " (cutoff:3.500A) 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 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 61 Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.606A pdb=" N LYS F 84 " --> pdb=" O ASP F 80 " (cutoff:3.500A) Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.334A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU F 117 " --> pdb=" O LYS F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 146 removed outlier: 3.837A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 194 removed outlier: 3.721A pdb=" N THR F 194 " --> pdb=" O MET F 190 " (cutoff:3.500A) Processing helix chain 'F' and resid 195 through 197 No H-bonds generated for 'chain 'F' and resid 195 through 197' Processing helix chain 'F' and resid 202 through 217 removed outlier: 4.370A pdb=" N ILE F 208 " --> pdb=" O ALA F 204 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ASP F 211 " --> pdb=" O GLU F 207 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLU F 214 " --> pdb=" O ARG F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 222 through 233 removed outlier: 3.623A pdb=" N GLU F 226 " --> pdb=" O ASP F 222 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 237 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.760A pdb=" N ARG F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 257' 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 285 Processing helix chain 'F' and resid 289 through 296 Processing helix chain 'F' and resid 301 through 306 removed outlier: 4.362A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 319 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'F' and resid 348 through 355 removed outlier: 6.032A pdb=" N THR F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 removed outlier: 3.651A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 368 through 374 removed outlier: 3.819A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 20 Processing helix chain 'E' and resid 29 through 39 removed outlier: 4.272A pdb=" N GLY E 33 " --> pdb=" O TYR E 29 " (cutoff:3.500A) removed outlier: 4.538A 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 'G' and resid 55 through 61 Processing helix chain 'G' and resid 78 through 92 removed outlier: 3.580A pdb=" N LYS G 84 " --> pdb=" O ASP G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 101 removed outlier: 3.571A pdb=" N HIS G 101 " --> pdb=" O PRO G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 126 removed outlier: 4.319A pdb=" N ARG G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLU G 117 " --> pdb=" O LYS G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 137 through 146 removed outlier: 3.834A pdb=" N LEU G 142 " --> pdb=" O ALA G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 Processing helix chain 'G' and resid 181 through 194 removed outlier: 3.726A pdb=" N THR G 194 " --> pdb=" O MET G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 195 through 197 No H-bonds generated for 'chain 'G' and resid 195 through 197' Processing helix chain 'G' and resid 202 through 217 removed outlier: 4.317A pdb=" N ILE G 208 " --> pdb=" O ALA G 204 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASP G 211 " --> pdb=" O GLU G 207 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLU G 214 " --> pdb=" O ARG G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 222 through 233 removed outlier: 3.619A pdb=" N GLU G 226 " --> pdb=" O ASP G 222 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 237 Processing helix chain 'G' and resid 252 through 260 removed outlier: 3.686A pdb=" N ARG G 256 " --> pdb=" O ASN G 252 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N CYS G 257 " --> pdb=" O GLU G 253 " (cutoff:3.500A) Proline residue: G 258 - end of helix No H-bonds generated for 'chain 'G' and resid 252 through 260' Processing helix chain 'G' and resid 261 through 262 No H-bonds generated for 'chain 'G' and resid 261 through 262' Processing helix chain 'G' and resid 263 through 268 Processing helix chain 'G' and resid 273 through 285 removed outlier: 3.503A pdb=" N CYS G 285 " --> pdb=" O SER G 281 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 296 Processing helix chain 'G' and resid 301 through 306 removed outlier: 4.393A pdb=" N TYR G 306 " --> pdb=" O THR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 308 through 319 Processing helix chain 'G' and resid 334 through 336 No H-bonds generated for 'chain 'G' and resid 334 through 336' Processing helix chain 'G' and resid 337 through 347 Processing helix chain 'G' and resid 348 through 355 removed outlier: 6.032A pdb=" N THR G 351 " --> pdb=" O SER G 348 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLN G 354 " --> pdb=" O THR G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 359 through 366 removed outlier: 3.658A pdb=" N GLU G 364 " --> pdb=" O GLN G 360 " (cutoff:3.500A) Processing helix chain 'G' and resid 368 through 374 removed outlier: 3.943A pdb=" N ARG G 372 " --> pdb=" O SER G 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.724A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 100 through 103 removed outlier: 4.108A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 163 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLY A 221 " --> pdb=" O THR A 241 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N THR A 241 " --> pdb=" O GLY A 221 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N TYR A 223 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N MET A 239 " --> pdb=" O TYR A 223 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N GLU A 225 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N ALA A 237 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA4, first strand: chain 'A' and resid 341 through 344 removed outlier: 6.497A pdb=" N SER A 347 " --> pdb=" O ARG A 343 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA6, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA7, first strand: chain 'A' and resid 700 through 703 Processing sheet with id=AA8, first strand: chain 'C' and resid 29 through 32 removed outlier: 4.130A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB3, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.418A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB5, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AB6, first strand: chain 'B' and resid 103 through 105 Processing sheet with id=AB7, first strand: chain 'D' and resid 12 through 16 removed outlier: 3.765A pdb=" N LEU D 40 " --> pdb=" O LEU D 48 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N LEU D 42 " --> pdb=" O LYS D 46 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LYS D 46 " --> pdb=" O LEU D 42 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 100 through 103 removed outlier: 3.924A pdb=" N GLN D 157 " --> pdb=" O PHE D 432 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY D 163 " --> pdb=" O ILE D 438 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLY D 227 " --> pdb=" O GLY D 236 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY D 236 " --> pdb=" O GLY D 227 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 209 Processing sheet with id=AC1, first strand: chain 'D' and resid 341 through 344 removed outlier: 6.556A pdb=" N SER D 347 " --> pdb=" O ARG D 343 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 377 through 382 Processing sheet with id=AC3, first strand: chain 'D' and resid 538 through 539 Processing sheet with id=AC4, first strand: chain 'D' and resid 700 through 703 Processing sheet with id=AC5, first strand: chain 'F' and resid 29 through 32 removed outlier: 3.508A pdb=" N LYS F 18 " --> pdb=" O ASP F 11 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N THR F 106 " --> pdb=" O CYS F 10 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AC7, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AC8, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AC9, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.470A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD2, first strand: chain 'E' and resid 26 through 28 Processing sheet with id=AD3, first strand: chain 'G' and resid 29 through 32 removed outlier: 3.945A pdb=" N THR G 106 " --> pdb=" O CYS G 10 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR G 103 " --> pdb=" O TYR G 133 " (cutoff:3.500A) removed outlier: 8.170A pdb=" N ALA G 135 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N LEU G 105 " --> pdb=" O ALA G 135 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AD5, first strand: chain 'G' and resid 71 through 72 Processing sheet with id=AD6, first strand: chain 'G' and resid 169 through 170 Processing sheet with id=AD7, first strand: chain 'G' and resid 169 through 170 removed outlier: 6.485A pdb=" N ILE G 151 " --> pdb=" O VAL G 298 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N SER G 300 " --> pdb=" O ILE G 151 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LEU G 153 " --> pdb=" O SER G 300 " (cutoff:3.500A) removed outlier: 6.708A 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 1178 hydrogen bonds defined for protein. 3216 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: 4.46 Time building geometry restraints manager: 2.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3886 1.32 - 1.44: 6271 1.44 - 1.56: 13375 1.56 - 1.69: 9 1.69 - 1.81: 242 Bond restraints: 23783 Sorted by residual: bond pdb=" CA EEP I 2 " pdb=" C EEP I 2 " ideal model delta sigma weight residual 1.572 1.452 0.120 2.00e-02 2.50e+03 3.61e+01 bond pdb=" CA EEP J 2 " pdb=" C EEP J 2 " ideal model delta sigma weight residual 1.572 1.452 0.120 2.00e-02 2.50e+03 3.59e+01 bond pdb=" CA EEP H 2 " pdb=" C EEP H 2 " ideal model delta sigma weight residual 1.572 1.456 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C HYP H 6 " pdb=" N ALA H 7 " ideal model delta sigma weight residual 1.329 1.374 -0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" C EEP H 2 " pdb=" O EEP H 2 " ideal model delta sigma weight residual 1.263 1.199 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 23778 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.16: 31813 3.16 - 6.33: 286 6.33 - 9.49: 29 9.49 - 12.65: 9 12.65 - 15.82: 1 Bond angle restraints: 32138 Sorted by residual: angle pdb=" C HYP I 6 " pdb=" N ALA I 7 " pdb=" CA ALA I 7 " ideal model delta sigma weight residual 121.70 110.42 11.28 1.80e+00 3.09e-01 3.93e+01 angle pdb=" C HYP J 6 " pdb=" N ALA J 7 " pdb=" CA ALA J 7 " ideal model delta sigma weight residual 121.70 110.72 10.98 1.80e+00 3.09e-01 3.72e+01 angle pdb=" C HYP H 6 " pdb=" N ALA H 7 " pdb=" CA ALA H 7 " ideal model delta sigma weight residual 121.70 111.01 10.69 1.80e+00 3.09e-01 3.52e+01 angle pdb=" N TRP I 1 " pdb=" CA TRP I 1 " pdb=" CB TRP I 1 " ideal model delta sigma weight residual 110.50 100.89 9.61 1.70e+00 3.46e-01 3.20e+01 angle pdb=" N TRP H 1 " pdb=" CA TRP H 1 " pdb=" CB TRP H 1 " ideal model delta sigma weight residual 110.50 101.48 9.02 1.70e+00 3.46e-01 2.81e+01 ... (remaining 32133 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.11: 14012 32.11 - 64.21: 271 64.21 - 96.32: 71 96.32 - 128.43: 3 128.43 - 160.53: 6 Dihedral angle restraints: 14363 sinusoidal: 5883 harmonic: 8480 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 -60.00 100.53 -160.53 1 2.00e+01 2.50e-03 4.66e+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 -60.00 100.43 -160.43 1 2.00e+01 2.50e-03 4.66e+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 -60.00 100.37 -160.37 1 2.00e+01 2.50e-03 4.66e+01 ... (remaining 14360 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 2678 0.053 - 0.106: 679 0.106 - 0.159: 145 0.159 - 0.212: 16 0.212 - 0.265: 2 Chirality restraints: 3520 Sorted by residual: chirality pdb=" CA CYS H 5 " pdb=" N CYS H 5 " pdb=" C CYS H 5 " pdb=" CB CYS H 5 " both_signs ideal model delta sigma weight residual False 2.51 2.78 -0.27 2.00e-01 2.50e+01 1.76e+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 2.73 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA CYS J 5 " pdb=" N CYS J 5 " pdb=" C CYS J 5 " pdb=" CB CYS J 5 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 3517 not shown) Planarity restraints: 4115 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 278 " -0.080 9.50e-02 1.11e+02 4.75e-02 1.31e+01 pdb=" NE ARG D 278 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 278 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG D 278 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG D 278 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 278 " -0.080 9.50e-02 1.11e+02 4.77e-02 1.30e+01 pdb=" NE ARG A 278 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG A 278 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG A 278 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG A 278 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 213 " -0.078 9.50e-02 1.11e+02 4.70e-02 1.30e+01 pdb=" NE ARG D 213 " 0.025 2.00e-02 2.50e+03 pdb=" CZ ARG D 213 " -0.060 2.00e-02 2.50e+03 pdb=" NH1 ARG D 213 " 0.021 2.00e-02 2.50e+03 pdb=" NH2 ARG D 213 " 0.017 2.00e-02 2.50e+03 ... (remaining 4112 not shown) Histogram of nonbonded interaction distances: 1.73 - 2.36: 31 2.36 - 3.00: 12140 3.00 - 3.63: 34565 3.63 - 4.27: 52880 4.27 - 4.90: 89654 Nonbonded interactions: 189270 Sorted by model distance: nonbonded pdb=" CD1 TRP H 1 " pdb=" SG CYS H 5 " model vdw 1.729 3.620 nonbonded pdb=" CD1 TRP I 1 " pdb=" SG CYS I 5 " model vdw 1.729 3.620 nonbonded pdb=" CD1 TRP J 1 " pdb=" SG CYS J 5 " model vdw 1.733 3.620 nonbonded pdb=" OE2 GLU A 476 " pdb=" NH1 ARG A 701 " model vdw 2.180 3.120 nonbonded pdb=" OD1 ASP C 11 " pdb=" OG1 THR C 106 " model vdw 2.194 3.040 ... (remaining 189265 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: 0.02 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: 2.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 21.200 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 23789 Z= 0.230 Angle : 0.855 15.815 32156 Z= 0.490 Chirality : 0.049 0.265 3520 Planarity : 0.007 0.076 4109 Dihedral : 14.783 160.535 8885 Min Nonbonded Distance : 1.729 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Rotamer: Outliers : 0.04 % Allowed : 0.08 % Favored : 99.88 % 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: -1.57 (0.14), residues: 2841 helix: -1.71 (0.11), residues: 1390 sheet: 0.21 (0.25), residues: 363 loop : -0.22 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.061 0.009 ARG D 278 TYR 0.033 0.004 TYR A 102 PHE 0.054 0.002 PHE A 564 TRP 0.041 0.004 TRP H 1 HIS 0.012 0.002 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00480 (23783) covalent geometry : angle 0.84860 (32138) hydrogen bonds : bond 0.14359 ( 1172) hydrogen bonds : angle 6.63636 ( 3216) link_TRANS : bond 0.01203 ( 6) link_TRANS : angle 4.42048 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 398 time to evaluate : 0.931 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: C 190 MET cc_start: 0.8029 (mtm) cc_final: 0.7569 (mtp) REVERT: C 246 GLN cc_start: 0.7848 (mt0) cc_final: 0.7603 (tt0) REVERT: D 118 ILE cc_start: 0.8962 (pt) cc_final: 0.8759 (tp) REVERT: D 487 ILE cc_start: 0.8189 (tt) cc_final: 0.6674 (tt) REVERT: E 110 ARG cc_start: 0.8051 (mtt-85) cc_final: 0.7666 (mmt90) outliers start: 1 outliers final: 0 residues processed: 399 average time/residue: 0.1874 time to fit residues: 111.1622 Evaluate side-chains 204 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 197 optimal weight: 20.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 307 ASN A 398 ASN A 410 ASN A 463 GLN A 464 GLN A 481 GLN A 497 ASN A 775 GLN C 59 GLN C 121 GLN C 128 ASN C 162 ASN C 296 ASN B 75 GLN B 147 HIS ** D 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 156 ASN D 264 GLN D 307 ASN D 398 ASN D 410 ASN D 463 GLN D 464 GLN D 481 GLN D 497 ASN D 639 GLN ** D 775 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 121 GLN F 280 ASN F 296 ASN E 75 GLN G 121 GLN G 296 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.081152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.056152 restraints weight = 74136.340| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.86 r_work: 0.2835 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 23789 Z= 0.139 Angle : 0.625 9.133 32156 Z= 0.326 Chirality : 0.044 0.193 3520 Planarity : 0.004 0.059 4109 Dihedral : 9.668 171.455 3229 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Rotamer: Outliers : 1.21 % Allowed : 5.04 % Favored : 93.76 % 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: 0.58 (0.15), residues: 2841 helix: 0.35 (0.13), residues: 1408 sheet: 0.39 (0.25), residues: 375 loop : 0.76 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 278 TYR 0.018 0.001 TYR E 89 PHE 0.025 0.002 PHE A 564 TRP 0.023 0.002 TRP J 1 HIS 0.012 0.001 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00308 (23783) covalent geometry : angle 0.62512 (32138) hydrogen bonds : bond 0.03995 ( 1172) hydrogen bonds : angle 4.80627 ( 3216) link_TRANS : bond 0.00421 ( 6) link_TRANS : angle 0.75118 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 234 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 ILE cc_start: 0.8982 (pt) cc_final: 0.8752 (tp) REVERT: A 132 MET cc_start: 0.8683 (ttt) cc_final: 0.8101 (tmm) REVERT: A 511 GLU cc_start: 0.8762 (tm-30) cc_final: 0.8546 (tt0) REVERT: A 555 ASP cc_start: 0.8082 (p0) cc_final: 0.7806 (p0) REVERT: C 82 MET cc_start: 0.8731 (tpt) cc_final: 0.8471 (tpt) REVERT: C 176 MET cc_start: 0.8542 (mmt) cc_final: 0.8318 (mmt) REVERT: C 313 MET cc_start: 0.9248 (mmm) cc_final: 0.8934 (tpt) REVERT: B 140 ASN cc_start: 0.9326 (t0) cc_final: 0.8923 (p0) REVERT: D 118 ILE cc_start: 0.9089 (pt) cc_final: 0.8819 (tp) REVERT: F 132 MET cc_start: 0.8749 (ttp) cc_final: 0.8460 (tmm) REVERT: E 110 ARG cc_start: 0.8331 (mtt-85) cc_final: 0.7837 (mmt90) REVERT: E 120 MET cc_start: 0.4326 (ptp) cc_final: 0.3746 (mtt) REVERT: G 299 MET cc_start: 0.8542 (mmt) cc_final: 0.8240 (mmt) outliers start: 30 outliers final: 13 residues processed: 248 average time/residue: 0.1632 time to fit residues: 64.0288 Evaluate side-chains 175 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain F residue 44 MET Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 180 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 40 optimal weight: 4.9990 chunk 234 optimal weight: 1.9990 chunk 188 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 110 optimal weight: 3.9990 chunk 251 optimal weight: 6.9990 chunk 77 optimal weight: 0.1980 chunk 257 optimal weight: 4.9990 chunk 111 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 ASN ** B 147 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN D 775 GLN G 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.054424 restraints weight = 74143.816| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.84 r_work: 0.2791 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23789 Z= 0.179 Angle : 0.596 7.960 32156 Z= 0.308 Chirality : 0.044 0.225 3520 Planarity : 0.004 0.053 4109 Dihedral : 9.211 178.545 3229 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.49 % Allowed : 6.61 % Favored : 91.90 % 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: 0.94 (0.16), residues: 2841 helix: 0.82 (0.14), residues: 1412 sheet: 0.45 (0.26), residues: 371 loop : 0.68 (0.19), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 41 TYR 0.014 0.001 TYR A 259 PHE 0.018 0.002 PHE A 564 TRP 0.015 0.002 TRP G 79 HIS 0.010 0.001 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.00416 (23783) covalent geometry : angle 0.59578 (32138) hydrogen bonds : bond 0.03886 ( 1172) hydrogen bonds : angle 4.64301 ( 3216) link_TRANS : bond 0.00148 ( 6) link_TRANS : angle 0.74176 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 180 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8538 (tpp) cc_final: 0.8166 (tpp) REVERT: A 555 ASP cc_start: 0.8320 (p0) cc_final: 0.8047 (p0) REVERT: A 662 ILE cc_start: 0.9523 (pt) cc_final: 0.9315 (mt) REVERT: C 101 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7438 (p-80) REVERT: C 313 MET cc_start: 0.9221 (mmm) cc_final: 0.8911 (tpt) REVERT: B 105 MET cc_start: 0.7960 (mmp) cc_final: 0.7218 (tpt) REVERT: D 118 ILE cc_start: 0.9073 (pt) cc_final: 0.8818 (tp) REVERT: D 323 MET cc_start: 0.8910 (mmm) cc_final: 0.8572 (mmm) REVERT: F 82 MET cc_start: 0.8827 (tpp) cc_final: 0.8341 (tpt) REVERT: F 132 MET cc_start: 0.8748 (ttp) cc_final: 0.8478 (tmm) REVERT: F 176 MET cc_start: 0.8955 (mmt) cc_final: 0.8739 (mmt) REVERT: E 19 PHE cc_start: 0.7623 (t80) cc_final: 0.6862 (t80) REVERT: E 110 ARG cc_start: 0.8320 (mtt-85) cc_final: 0.7162 (mmt90) REVERT: G 117 GLU cc_start: 0.8626 (mt-10) cc_final: 0.8381 (mt-10) REVERT: G 299 MET cc_start: 0.8503 (mmt) cc_final: 0.8251 (mmt) outliers start: 37 outliers final: 16 residues processed: 208 average time/residue: 0.1510 time to fit residues: 51.0399 Evaluate side-chains 181 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 164 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain C residue 101 HIS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 257 optimal weight: 0.9990 chunk 219 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 165 optimal weight: 10.0000 chunk 231 optimal weight: 0.6980 chunk 168 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 638 HIS B 8 GLN F 225 ASN G 40 HIS G 225 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.054372 restraints weight = 74417.146| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.82 r_work: 0.2788 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23789 Z= 0.150 Angle : 0.560 7.662 32156 Z= 0.288 Chirality : 0.043 0.232 3520 Planarity : 0.004 0.049 4109 Dihedral : 8.653 175.695 3229 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 1.69 % Allowed : 7.86 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.21 (0.16), residues: 2841 helix: 1.17 (0.14), residues: 1389 sheet: 0.33 (0.26), residues: 371 loop : 0.73 (0.19), residues: 1081 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 37 TYR 0.011 0.001 TYR A 259 PHE 0.016 0.001 PHE A 564 TRP 0.014 0.002 TRP G 79 HIS 0.009 0.001 HIS B 147 Details of bonding type rmsd covalent geometry : bond 0.00347 (23783) covalent geometry : angle 0.55986 (32138) hydrogen bonds : bond 0.03532 ( 1172) hydrogen bonds : angle 4.51803 ( 3216) link_TRANS : bond 0.00111 ( 6) link_TRANS : angle 0.76715 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 1.023 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 211 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8500 (p) REVERT: A 305 MET cc_start: 0.8524 (tpp) cc_final: 0.8063 (tpp) REVERT: A 467 MET cc_start: 0.9085 (tpp) cc_final: 0.8884 (tpp) REVERT: A 555 ASP cc_start: 0.8429 (p0) cc_final: 0.8129 (p0) REVERT: C 313 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8918 (tpt) REVERT: B 105 MET cc_start: 0.8003 (mmp) cc_final: 0.7205 (tpp) REVERT: B 147 HIS cc_start: 0.7178 (OUTLIER) cc_final: 0.6859 (p90) REVERT: D 118 ILE cc_start: 0.9102 (pt) cc_final: 0.8820 (tp) REVERT: D 323 MET cc_start: 0.8951 (mmm) cc_final: 0.8620 (mmm) REVERT: D 484 TRP cc_start: 0.7104 (m-10) cc_final: 0.6314 (m-10) REVERT: F 176 MET cc_start: 0.8952 (mmt) cc_final: 0.8744 (mmt) REVERT: E 19 PHE cc_start: 0.7454 (t80) cc_final: 0.6711 (t80) REVERT: G 299 MET cc_start: 0.8514 (mmt) cc_final: 0.8234 (mmt) outliers start: 42 outliers final: 20 residues processed: 210 average time/residue: 0.1386 time to fit residues: 48.3211 Evaluate side-chains 185 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 446 ILE Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 218 optimal weight: 3.9990 chunk 210 optimal weight: 0.5980 chunk 223 optimal weight: 0.8980 chunk 179 optimal weight: 4.9990 chunk 248 optimal weight: 0.3980 chunk 254 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 166 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 474 GLN B 8 GLN D 216 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.080041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054728 restraints weight = 73237.971| |-----------------------------------------------------------------------------| r_work (start): 0.2943 rms_B_bonded: 2.87 r_work: 0.2798 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23789 Z= 0.124 Angle : 0.536 7.084 32156 Z= 0.274 Chirality : 0.042 0.246 3520 Planarity : 0.004 0.049 4109 Dihedral : 8.023 155.682 3229 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.37 % Allowed : 8.38 % Favored : 90.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.35 (0.16), residues: 2841 helix: 1.33 (0.14), residues: 1372 sheet: 0.34 (0.27), residues: 365 loop : 0.75 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 37 TYR 0.011 0.001 TYR A 259 PHE 0.015 0.001 PHE A 564 TRP 0.013 0.001 TRP G 79 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00285 (23783) covalent geometry : angle 0.53571 (32138) hydrogen bonds : bond 0.03352 ( 1172) hydrogen bonds : angle 4.43081 ( 3216) link_TRANS : bond 0.00115 ( 6) link_TRANS : angle 0.75717 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 176 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.8807 (OUTLIER) cc_final: 0.8472 (p) REVERT: A 305 MET cc_start: 0.8448 (tpp) cc_final: 0.8020 (tpp) REVERT: A 555 ASP cc_start: 0.8486 (p0) cc_final: 0.8203 (p0) REVERT: A 682 LEU cc_start: 0.9132 (mt) cc_final: 0.8841 (mm) REVERT: C 47 MET cc_start: 0.7872 (ppp) cc_final: 0.7669 (ppp) REVERT: C 167 GLU cc_start: 0.8929 (OUTLIER) cc_final: 0.8571 (mp0) REVERT: C 313 MET cc_start: 0.9193 (mmm) cc_final: 0.8909 (tpt) REVERT: C 361 GLU cc_start: 0.8196 (mp0) cc_final: 0.7970 (mp0) REVERT: B 105 MET cc_start: 0.8042 (mmp) cc_final: 0.7225 (tpp) REVERT: B 147 HIS cc_start: 0.7203 (OUTLIER) cc_final: 0.6874 (p90) REVERT: D 118 ILE cc_start: 0.9054 (pt) cc_final: 0.8792 (tp) REVERT: D 132 MET cc_start: 0.8409 (tpp) cc_final: 0.8158 (tpp) REVERT: D 323 MET cc_start: 0.8964 (mmm) cc_final: 0.8639 (mmm) REVERT: D 371 MET cc_start: 0.9279 (mmt) cc_final: 0.8973 (tpp) REVERT: D 749 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8777 (mp) REVERT: F 167 GLU cc_start: 0.8699 (mt-10) cc_final: 0.8463 (mm-30) REVERT: F 176 MET cc_start: 0.8954 (mmt) cc_final: 0.8732 (mmt) REVERT: E 19 PHE cc_start: 0.7501 (t80) cc_final: 0.6746 (t80) REVERT: E 110 ARG cc_start: 0.8336 (mmt180) cc_final: 0.8032 (mmt180) REVERT: E 120 MET cc_start: 0.3417 (ptt) cc_final: 0.3086 (ppp) REVERT: G 119 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8477 (mtm) REVERT: G 299 MET cc_start: 0.8522 (mmt) cc_final: 0.8208 (mmt) outliers start: 34 outliers final: 19 residues processed: 200 average time/residue: 0.1413 time to fit residues: 47.4038 Evaluate side-chains 186 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain B residue 8 GLN Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 156 optimal weight: 6.9990 chunk 212 optimal weight: 0.0980 chunk 61 optimal weight: 5.9990 chunk 158 optimal weight: 2.9990 chunk 254 optimal weight: 4.9990 chunk 273 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 58 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 89 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 8 GLN G 225 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.079697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.054234 restraints weight = 74106.819| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.84 r_work: 0.2785 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23789 Z= 0.150 Angle : 0.553 11.274 32156 Z= 0.282 Chirality : 0.042 0.258 3520 Planarity : 0.004 0.046 4109 Dihedral : 7.721 141.683 3229 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 1.49 % Allowed : 8.78 % Favored : 89.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.32 (0.16), residues: 2841 helix: 1.36 (0.14), residues: 1392 sheet: 0.34 (0.27), residues: 365 loop : 0.65 (0.19), residues: 1084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 372 TYR 0.013 0.001 TYR A 259 PHE 0.027 0.001 PHE B 12 TRP 0.013 0.002 TRP D 484 HIS 0.006 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00348 (23783) covalent geometry : angle 0.55329 (32138) hydrogen bonds : bond 0.03411 ( 1172) hydrogen bonds : angle 4.42569 ( 3216) link_TRANS : bond 0.00106 ( 6) link_TRANS : angle 0.75298 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8513 (p) REVERT: A 305 MET cc_start: 0.8459 (tpp) cc_final: 0.7976 (tpp) REVERT: A 555 ASP cc_start: 0.8475 (p0) cc_final: 0.8206 (p0) REVERT: A 682 LEU cc_start: 0.9138 (mt) cc_final: 0.8815 (mm) REVERT: A 715 MET cc_start: 0.8313 (mmm) cc_final: 0.7880 (mmm) REVERT: C 47 MET cc_start: 0.7951 (ppp) cc_final: 0.7675 (ppp) REVERT: C 167 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8549 (mp0) REVERT: C 313 MET cc_start: 0.9196 (OUTLIER) cc_final: 0.8918 (tpt) REVERT: B 89 TYR cc_start: 0.8269 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 105 MET cc_start: 0.8056 (mmp) cc_final: 0.7347 (tpp) REVERT: B 147 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6852 (p90) REVERT: D 323 MET cc_start: 0.8982 (mmm) cc_final: 0.8693 (mmm) REVERT: D 371 MET cc_start: 0.9284 (mmt) cc_final: 0.8999 (tpp) REVERT: D 484 TRP cc_start: 0.7143 (m-10) cc_final: 0.6364 (m-10) REVERT: D 749 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8773 (mp) REVERT: F 176 MET cc_start: 0.8954 (mmt) cc_final: 0.8734 (mmt) REVERT: E 19 PHE cc_start: 0.7504 (t80) cc_final: 0.6808 (t80) REVERT: E 110 ARG cc_start: 0.8390 (mmt180) cc_final: 0.8047 (mmt180) REVERT: E 120 MET cc_start: 0.3360 (ptt) cc_final: 0.3119 (pmm) REVERT: G 119 MET cc_start: 0.8909 (OUTLIER) cc_final: 0.8525 (mtm) REVERT: G 299 MET cc_start: 0.8534 (mmt) cc_final: 0.8237 (mmt) outliers start: 37 outliers final: 21 residues processed: 194 average time/residue: 0.1445 time to fit residues: 47.0972 Evaluate side-chains 183 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 520 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 700 SER Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 119 MET Chi-restraints excluded: chain G residue 225 ASN Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 97 optimal weight: 4.9990 chunk 26 optimal weight: 7.9990 chunk 176 optimal weight: 0.5980 chunk 182 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 192 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 233 optimal weight: 4.9990 chunk 191 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN D 216 ASN D 638 HIS G 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.077298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.051550 restraints weight = 75102.447| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.87 r_work: 0.2717 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.061 23789 Z= 0.358 Angle : 0.697 10.685 32156 Z= 0.356 Chirality : 0.049 0.298 3520 Planarity : 0.005 0.065 4109 Dihedral : 8.168 149.177 3229 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.41 % Allowed : 9.31 % Favored : 89.28 % 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: 0.90 (0.16), residues: 2841 helix: 1.11 (0.14), residues: 1388 sheet: 0.04 (0.26), residues: 394 loop : 0.34 (0.19), residues: 1059 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 256 TYR 0.022 0.002 TYR A 259 PHE 0.051 0.002 PHE D 564 TRP 0.019 0.002 TRP F 340 HIS 0.008 0.002 HIS D 81 Details of bonding type rmsd covalent geometry : bond 0.00825 (23783) covalent geometry : angle 0.69666 (32138) hydrogen bonds : bond 0.04321 ( 1172) hydrogen bonds : angle 4.73810 ( 3216) link_TRANS : bond 0.00340 ( 6) link_TRANS : angle 0.69675 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 159 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.8886 (OUTLIER) cc_final: 0.8664 (p) REVERT: A 305 MET cc_start: 0.8599 (tpp) cc_final: 0.8360 (tpp) REVERT: C 47 MET cc_start: 0.7685 (ppp) cc_final: 0.7336 (ppp) REVERT: C 167 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8516 (mp0) REVERT: C 313 MET cc_start: 0.9260 (OUTLIER) cc_final: 0.8990 (tpt) REVERT: B 105 MET cc_start: 0.7940 (mmp) cc_final: 0.7098 (tpp) REVERT: B 147 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6927 (p90) REVERT: D 255 GLU cc_start: 0.8816 (pm20) cc_final: 0.8431 (tm-30) REVERT: D 484 TRP cc_start: 0.7242 (m-10) cc_final: 0.6578 (m-10) REVERT: D 749 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8564 (mm) REVERT: E 19 PHE cc_start: 0.7443 (t80) cc_final: 0.6805 (t80) REVERT: E 110 ARG cc_start: 0.8407 (mmt180) cc_final: 0.8041 (mmt90) REVERT: E 120 MET cc_start: 0.3453 (ptt) cc_final: 0.3043 (pmm) REVERT: G 299 MET cc_start: 0.8559 (mmt) cc_final: 0.8312 (mmt) outliers start: 35 outliers final: 20 residues processed: 188 average time/residue: 0.1471 time to fit residues: 45.6724 Evaluate side-chains 177 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain C residue 313 MET Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 24 optimal weight: 0.6980 chunk 229 optimal weight: 0.9980 chunk 163 optimal weight: 0.9990 chunk 280 optimal weight: 1.9990 chunk 176 optimal weight: 0.7980 chunk 203 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 279 optimal weight: 2.9990 chunk 277 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 143 optimal weight: 0.9980 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 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.079677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.053987 restraints weight = 73604.755| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 2.89 r_work: 0.2785 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.3709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23789 Z= 0.118 Angle : 0.562 10.259 32156 Z= 0.286 Chirality : 0.042 0.260 3520 Planarity : 0.004 0.046 4109 Dihedral : 7.574 129.201 3229 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 1.21 % Allowed : 10.11 % Favored : 88.68 % 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: 1.22 (0.16), residues: 2841 helix: 1.45 (0.15), residues: 1356 sheet: 0.11 (0.27), residues: 365 loop : 0.43 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 372 TYR 0.011 0.001 TYR A 259 PHE 0.020 0.001 PHE D 564 TRP 0.015 0.001 TRP G 340 HIS 0.007 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00273 (23783) covalent geometry : angle 0.56155 (32138) hydrogen bonds : bond 0.03356 ( 1172) hydrogen bonds : angle 4.47118 ( 3216) link_TRANS : bond 0.00131 ( 6) link_TRANS : angle 0.77540 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 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: 30 poor density : 166 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 211 THR cc_start: 0.8856 (OUTLIER) cc_final: 0.8539 (p) REVERT: A 305 MET cc_start: 0.8462 (tpp) cc_final: 0.8020 (tpp) REVERT: A 478 MET cc_start: 0.8852 (mmp) cc_final: 0.8542 (mmp) REVERT: A 682 LEU cc_start: 0.9194 (mt) cc_final: 0.8861 (mm) REVERT: A 788 MET cc_start: 0.9618 (mpp) cc_final: 0.9406 (pmm) REVERT: C 47 MET cc_start: 0.8006 (ppp) cc_final: 0.7715 (ppp) REVERT: C 167 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8587 (mp0) REVERT: C 313 MET cc_start: 0.9206 (mmm) cc_final: 0.8930 (tpt) REVERT: B 105 MET cc_start: 0.8003 (mmp) cc_final: 0.7222 (tpp) REVERT: B 147 HIS cc_start: 0.7226 (OUTLIER) cc_final: 0.6879 (p90) REVERT: D 371 MET cc_start: 0.9279 (mmt) cc_final: 0.9001 (tpp) REVERT: D 484 TRP cc_start: 0.7281 (m-10) cc_final: 0.6772 (m-10) REVERT: D 749 ILE cc_start: 0.9030 (OUTLIER) cc_final: 0.8509 (mm) REVERT: E 19 PHE cc_start: 0.7454 (t80) cc_final: 0.6805 (t80) REVERT: E 110 ARG cc_start: 0.8396 (mmt180) cc_final: 0.8031 (mmt90) REVERT: E 120 MET cc_start: 0.3456 (ptt) cc_final: 0.3008 (pmm) REVERT: G 132 MET cc_start: 0.8717 (ttt) cc_final: 0.8362 (ttt) REVERT: G 187 ASP cc_start: 0.8566 (m-30) cc_final: 0.8338 (m-30) REVERT: G 299 MET cc_start: 0.8488 (mmt) cc_final: 0.8169 (mmt) outliers start: 30 outliers final: 16 residues processed: 188 average time/residue: 0.1388 time to fit residues: 43.7678 Evaluate side-chains 172 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 257 CYS Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 7.9990 chunk 68 optimal weight: 6.9990 chunk 84 optimal weight: 0.5980 chunk 120 optimal weight: 30.0000 chunk 155 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 139 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 overall best weight: 3.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.077105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.051389 restraints weight = 75172.621| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.88 r_work: 0.2709 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 23789 Z= 0.343 Angle : 0.716 9.716 32156 Z= 0.365 Chirality : 0.048 0.302 3520 Planarity : 0.005 0.048 4109 Dihedral : 8.087 143.790 3229 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.25 % Allowed : 10.60 % Favored : 88.15 % 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: 0.80 (0.16), residues: 2841 helix: 1.19 (0.14), residues: 1350 sheet: -0.13 (0.26), residues: 394 loop : 0.12 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 372 TYR 0.021 0.002 TYR A 259 PHE 0.042 0.002 PHE A 564 TRP 0.018 0.002 TRP F 340 HIS 0.008 0.001 HIS D 81 Details of bonding type rmsd covalent geometry : bond 0.00791 (23783) covalent geometry : angle 0.71607 (32138) hydrogen bonds : bond 0.04400 ( 1172) hydrogen bonds : angle 4.80954 ( 3216) link_TRANS : bond 0.00321 ( 6) link_TRANS : angle 0.79936 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 148 time to evaluate : 0.871 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8610 (tpp) cc_final: 0.8371 (tpp) REVERT: A 478 MET cc_start: 0.8767 (mmp) cc_final: 0.8377 (mmp) REVERT: C 47 MET cc_start: 0.7806 (ppp) cc_final: 0.7444 (ppp) REVERT: C 167 GLU cc_start: 0.8917 (OUTLIER) cc_final: 0.8511 (mp0) REVERT: C 313 MET cc_start: 0.9255 (mmm) cc_final: 0.8968 (tpt) REVERT: B 105 MET cc_start: 0.7951 (mmp) cc_final: 0.7138 (tpp) REVERT: B 120 MET cc_start: 0.7132 (pmm) cc_final: 0.6830 (pmm) REVERT: B 147 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.7015 (p90) REVERT: D 255 GLU cc_start: 0.8798 (pm20) cc_final: 0.8408 (tm-30) REVERT: D 439 TYR cc_start: 0.8695 (OUTLIER) cc_final: 0.8370 (p90) REVERT: D 484 TRP cc_start: 0.7189 (m-10) cc_final: 0.6781 (m-10) REVERT: D 749 ILE cc_start: 0.9052 (OUTLIER) cc_final: 0.8773 (mp) REVERT: E 19 PHE cc_start: 0.7401 (t80) cc_final: 0.6736 (t80) REVERT: E 120 MET cc_start: 0.3474 (ptt) cc_final: 0.3092 (pmm) outliers start: 31 outliers final: 19 residues processed: 174 average time/residue: 0.1433 time to fit residues: 42.0794 Evaluate side-chains 168 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 439 TYR Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain F residue 260 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 263 optimal weight: 0.8980 chunk 157 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 252 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 142 optimal weight: 0.9990 chunk 177 optimal weight: 0.8980 chunk 144 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.079541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.053755 restraints weight = 74742.536| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 2.89 r_work: 0.2784 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.3895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23789 Z= 0.116 Angle : 0.570 10.999 32156 Z= 0.290 Chirality : 0.042 0.260 3520 Planarity : 0.004 0.047 4109 Dihedral : 7.433 123.951 3229 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 0.93 % Allowed : 11.00 % Favored : 88.07 % 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: 1.22 (0.16), residues: 2841 helix: 1.52 (0.15), residues: 1338 sheet: 0.06 (0.28), residues: 344 loop : 0.35 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 372 TYR 0.010 0.001 TYR D 263 PHE 0.020 0.001 PHE B 12 TRP 0.020 0.002 TRP A 484 HIS 0.008 0.001 HIS A 418 Details of bonding type rmsd covalent geometry : bond 0.00265 (23783) covalent geometry : angle 0.56990 (32138) hydrogen bonds : bond 0.03329 ( 1172) hydrogen bonds : angle 4.50038 ( 3216) link_TRANS : bond 0.00123 ( 6) link_TRANS : angle 0.78783 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 0.910 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 305 MET cc_start: 0.8486 (tpp) cc_final: 0.7965 (tpp) REVERT: A 715 MET cc_start: 0.8457 (mmm) cc_final: 0.7860 (mmm) REVERT: C 47 MET cc_start: 0.7987 (ppp) cc_final: 0.7613 (ppp) REVERT: C 167 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8605 (mp0) REVERT: C 313 MET cc_start: 0.9202 (mmm) cc_final: 0.8940 (tpt) REVERT: B 105 MET cc_start: 0.8007 (mmp) cc_final: 0.7176 (tpp) REVERT: B 147 HIS cc_start: 0.7328 (OUTLIER) cc_final: 0.6970 (p90) REVERT: D 255 GLU cc_start: 0.8716 (pm20) cc_final: 0.8421 (tm-30) REVERT: D 371 MET cc_start: 0.9295 (mmt) cc_final: 0.8982 (tpp) REVERT: D 484 TRP cc_start: 0.7213 (m-10) cc_final: 0.6739 (m-10) REVERT: D 749 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8511 (mm) REVERT: E 19 PHE cc_start: 0.7373 (t80) cc_final: 0.6738 (t80) REVERT: E 110 ARG cc_start: 0.8358 (mmt180) cc_final: 0.8023 (mmt180) REVERT: E 120 MET cc_start: 0.3957 (ptt) cc_final: 0.3412 (pmm) REVERT: G 132 MET cc_start: 0.8732 (ttt) cc_final: 0.8383 (ttt) REVERT: G 187 ASP cc_start: 0.8547 (m-30) cc_final: 0.8319 (m-30) outliers start: 23 outliers final: 16 residues processed: 174 average time/residue: 0.1436 time to fit residues: 41.8637 Evaluate side-chains 170 residues out of total 2504 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 THR Chi-restraints excluded: chain A residue 439 TYR Chi-restraints excluded: chain A residue 510 ASP Chi-restraints excluded: chain A residue 521 ASP Chi-restraints excluded: chain A residue 630 LYS Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 132 MET Chi-restraints excluded: chain C residue 167 GLU Chi-restraints excluded: chain C residue 271 SER Chi-restraints excluded: chain B residue 93 PHE Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain D residue 234 ILE Chi-restraints excluded: chain D residue 749 ILE Chi-restraints excluded: chain F residue 101 HIS Chi-restraints excluded: chain F residue 106 THR Chi-restraints excluded: chain G residue 100 GLU Chi-restraints excluded: chain G residue 101 HIS Chi-restraints excluded: chain G residue 257 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 285 random chunks: chunk 48 optimal weight: 4.9990 chunk 117 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 263 optimal weight: 8.9990 chunk 160 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 273 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 128 optimal weight: 0.0470 chunk 32 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 overall best weight: 1.5482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 310 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.078663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.053335 restraints weight = 74255.291| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.86 r_work: 0.2764 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 23789 Z= 0.165 Angle : 0.593 10.430 32156 Z= 0.300 Chirality : 0.043 0.270 3520 Planarity : 0.004 0.047 4109 Dihedral : 7.432 127.420 3229 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.93 % Allowed : 11.20 % Favored : 87.87 % 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: 1.24 (0.16), residues: 2841 helix: 1.53 (0.15), residues: 1338 sheet: 0.10 (0.28), residues: 344 loop : 0.36 (0.18), residues: 1159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 372 TYR 0.014 0.001 TYR A 259 PHE 0.024 0.001 PHE D 564 TRP 0.019 0.002 TRP A 484 HIS 0.010 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00385 (23783) covalent geometry : angle 0.59266 (32138) hydrogen bonds : bond 0.03498 ( 1172) hydrogen bonds : angle 4.51690 ( 3216) link_TRANS : bond 0.00128 ( 6) link_TRANS : angle 0.79139 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6624.91 seconds wall clock time: 113 minutes 58.49 seconds (6838.49 seconds total)