Starting phenix.real_space_refine on Mon Sep 30 08:09:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/09_2024/7uuw_26805.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/09_2024/7uuw_26805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/09_2024/7uuw_26805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/09_2024/7uuw_26805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/09_2024/7uuw_26805.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/09_2024/7uuw_26805.cif" } resolution = 3.36 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.066 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 12 5.49 5 Mg 6 5.21 5 S 192 5.16 5 C 15654 2.51 5 N 4242 2.21 5 O 4746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24852 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} 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: "G" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "H" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "I" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "L" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "Z" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" 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} Time building chain proxies: 13.71, per 1000 atoms: 0.55 Number of scatterers: 24852 At special positions: 0 Unit cell: (102.384, 120.528, 222.912, 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 192 16.00 P 12 15.00 Mg 6 11.99 O 4746 8.00 N 4242 7.00 C 15654 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 Time building additional restraints: 7.99 Conformation dependent library (CDL) restraints added in 3.0 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 36 sheets defined 59.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.68 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.762A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.513A pdb=" N LEU A 65 " --> pdb=" O ARG A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.781A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 284 through 285 No H-bonds generated for 'chain 'A' and resid 284 through 285' Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.068A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.513A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.780A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.784A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 284 through 285 No H-bonds generated for 'chain 'B' and resid 284 through 285' Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.737A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.068A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.582A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.780A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.590A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.027A 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 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.068A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU D 65 " --> pdb=" O ARG D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.780A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 257' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.069A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU E 65 " --> pdb=" O ARG E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.781A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 257' Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 284 through 285 No H-bonds generated for 'chain 'E' and resid 284 through 285' Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 319 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.068A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU F 65 " --> pdb=" O ARG F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.781A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.782A pdb=" N ARG F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 3.603A 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 261 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.588A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.027A 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 348 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.067A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 691 through 696 Processing helix chain 'G' and resid 714 through 738 Processing helix chain 'G' and resid 744 through 773 Processing helix chain 'G' and resid 776 through 810 removed outlier: 3.621A pdb=" N LYS G 780 " --> pdb=" O SER G 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 810 " --> pdb=" O VAL G 806 " (cutoff:3.500A) Processing helix chain 'G' and resid 818 through 848 removed outlier: 4.250A pdb=" N SER G 823 " --> pdb=" O ASP G 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN G 837 " --> pdb=" O THR G 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G 838 " --> pdb=" O ALA G 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS G 840 " --> pdb=" O VAL G 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 841 " --> pdb=" O GLN G 837 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 696 Processing helix chain 'H' and resid 714 through 738 Processing helix chain 'H' and resid 744 through 773 Processing helix chain 'H' and resid 776 through 810 removed outlier: 3.621A pdb=" N LYS H 780 " --> pdb=" O SER H 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY H 810 " --> pdb=" O VAL H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 818 through 848 removed outlier: 4.252A pdb=" N SER H 823 " --> pdb=" O ASP H 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU H 824 " --> pdb=" O SER H 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN H 837 " --> pdb=" O THR H 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR H 838 " --> pdb=" O ALA H 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS H 840 " --> pdb=" O VAL H 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 841 " --> pdb=" O GLN H 837 " (cutoff:3.500A) Processing helix chain 'I' and resid 691 through 696 Processing helix chain 'I' and resid 714 through 738 Processing helix chain 'I' and resid 744 through 773 Processing helix chain 'I' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS I 780 " --> pdb=" O SER I 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY I 810 " --> pdb=" O VAL I 806 " (cutoff:3.500A) Processing helix chain 'I' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER I 823 " --> pdb=" O ASP I 819 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU I 824 " --> pdb=" O SER I 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN I 837 " --> pdb=" O THR I 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR I 838 " --> pdb=" O ALA I 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS I 840 " --> pdb=" O VAL I 836 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 841 " --> pdb=" O GLN I 837 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 696 Processing helix chain 'K' and resid 714 through 738 Processing helix chain 'K' and resid 744 through 773 Processing helix chain 'K' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS K 780 " --> pdb=" O SER K 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY K 810 " --> pdb=" O VAL K 806 " (cutoff:3.500A) Processing helix chain 'K' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER K 823 " --> pdb=" O ASP K 819 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU K 824 " --> pdb=" O SER K 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN K 837 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR K 838 " --> pdb=" O ALA K 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS K 840 " --> pdb=" O VAL K 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 841 " --> pdb=" O GLN K 837 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 696 Processing helix chain 'L' and resid 714 through 738 Processing helix chain 'L' and resid 744 through 773 Processing helix chain 'L' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS L 780 " --> pdb=" O SER L 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY L 810 " --> pdb=" O VAL L 806 " (cutoff:3.500A) Processing helix chain 'L' and resid 818 through 848 removed outlier: 4.250A pdb=" N SER L 823 " --> pdb=" O ASP L 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU L 824 " --> pdb=" O SER L 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN L 837 " --> pdb=" O THR L 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR L 838 " --> pdb=" O ALA L 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS L 840 " --> pdb=" O VAL L 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 841 " --> pdb=" O GLN L 837 " (cutoff:3.500A) Processing helix chain 'Z' and resid 691 through 696 Processing helix chain 'Z' and resid 714 through 738 Processing helix chain 'Z' and resid 744 through 773 Processing helix chain 'Z' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS Z 780 " --> pdb=" O SER Z 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY Z 810 " --> pdb=" O VAL Z 806 " (cutoff:3.500A) Processing helix chain 'Z' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER Z 823 " --> pdb=" O ASP Z 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU Z 824 " --> pdb=" O SER Z 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN Z 837 " --> pdb=" O THR Z 833 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR Z 838 " --> pdb=" O ALA Z 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS Z 840 " --> pdb=" O VAL Z 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Z 841 " --> pdb=" O GLN Z 837 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.064A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.521A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.129A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.520A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.064A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.550A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 7.130A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 7.064A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.510A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AC2, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.528A pdb=" N GLN D 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL F 298 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC7, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC9, first strand: chain 'F' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AD2, first strand: chain 'F' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET F 176 " --> pdb=" O ASN F 162 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'G' and resid 697 through 698 Processing sheet with id=AD5, first strand: chain 'H' and resid 697 through 698 Processing sheet with id=AD6, first strand: chain 'I' and resid 697 through 698 Processing sheet with id=AD7, first strand: chain 'K' and resid 697 through 698 Processing sheet with id=AD8, first strand: chain 'L' and resid 697 through 698 Processing sheet with id=AD9, first strand: chain 'Z' and resid 697 through 698 1300 hydrogen bonds defined for protein. 3684 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: 10.41 Time building geometry restraints manager: 7.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8112 1.34 - 1.46: 5463 1.46 - 1.58: 11373 1.58 - 1.70: 18 1.70 - 1.82: 330 Bond restraints: 25296 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.11e+00 ... (remaining 25291 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.78: 33806 2.78 - 5.57: 409 5.57 - 8.35: 15 8.35 - 11.13: 0 11.13 - 13.92: 12 Bond angle restraints: 34242 Sorted by residual: angle pdb=" CB MET F 325 " pdb=" CG MET F 325 " pdb=" SD MET F 325 " ideal model delta sigma weight residual 112.70 98.78 13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 98.80 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 98.80 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 98.81 13.89 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 98.81 13.89 3.00e+00 1.11e-01 2.14e+01 ... (remaining 34237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 14910 34.41 - 68.82: 444 68.82 - 103.24: 48 103.24 - 137.65: 6 137.65 - 172.06: 12 Dihedral angle restraints: 15420 sinusoidal: 6222 harmonic: 9198 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.06 -172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.06 -172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.04 -172.04 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 15417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2192 0.034 - 0.068: 1232 0.068 - 0.103: 352 0.103 - 0.137: 113 0.137 - 0.171: 23 Chirality restraints: 3912 Sorted by residual: chirality pdb=" CA MET E 325 " pdb=" N MET E 325 " pdb=" C MET E 325 " pdb=" CB MET E 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA MET C 325 " pdb=" N MET C 325 " pdb=" C MET C 325 " pdb=" CB MET C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA MET B 325 " pdb=" N MET B 325 " pdb=" C MET B 325 " pdb=" CB MET B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3909 not shown) Planarity restraints: 4338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO E 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO D 243 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.022 5.00e-02 4.00e+02 ... (remaining 4335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2987 2.74 - 3.28: 24061 3.28 - 3.82: 39496 3.82 - 4.36: 49656 4.36 - 4.90: 88228 Nonbonded interactions: 204428 Sorted by model distance: nonbonded pdb=" O GLY A 156 " pdb=" OG1 THR A 303 " model vdw 2.202 3.040 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.203 3.040 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.203 3.040 nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.203 3.040 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.204 3.040 ... (remaining 204423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' selection = chain 'Z' } 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: 2.490 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: 0.030 Extract box with map and model: 0.860 Check model and map are aligned: 0.190 Set scattering table: 0.230 Process input model: 57.050 Find NCS groups from input model: 3.150 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.007 0.054 25296 Z= 0.463 Angle : 0.750 13.916 34242 Z= 0.392 Chirality : 0.046 0.171 3912 Planarity : 0.004 0.040 4338 Dihedral : 17.000 172.062 9480 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.34 % Allowed : 3.53 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3096 helix: 0.48 (0.13), residues: 1656 sheet: -1.68 (0.27), residues: 366 loop : -0.22 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 340 HIS 0.003 0.001 HIS C 87 PHE 0.013 0.001 PHE Z 697 TYR 0.014 0.002 TYR D 279 ARG 0.004 0.001 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 329 time to evaluate : 3.071 Fit side-chains REVERT: A 118 LYS cc_start: 0.8375 (mttm) cc_final: 0.7909 (mmmt) REVERT: A 119 MET cc_start: 0.8288 (mtm) cc_final: 0.7662 (mtp) REVERT: A 157 ASP cc_start: 0.8839 (t0) cc_final: 0.8633 (t0) REVERT: A 176 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: A 211 ASP cc_start: 0.8633 (t0) cc_final: 0.8254 (t0) REVERT: A 227 MET cc_start: 0.8660 (mmm) cc_final: 0.8231 (mmt) REVERT: B 123 MET cc_start: 0.8667 (mmt) cc_final: 0.8386 (mmm) REVERT: B 191 LYS cc_start: 0.7348 (tttp) cc_final: 0.6910 (tttt) REVERT: B 313 MET cc_start: 0.8219 (ttt) cc_final: 0.7841 (ttt) REVERT: B 349 LEU cc_start: 0.8477 (mt) cc_final: 0.8178 (mt) REVERT: C 82 MET cc_start: 0.8551 (tpt) cc_final: 0.8341 (tpt) REVERT: C 211 ASP cc_start: 0.8594 (t0) cc_final: 0.8265 (t0) REVERT: C 313 MET cc_start: 0.8000 (ttt) cc_final: 0.7738 (ttm) REVERT: D 119 MET cc_start: 0.8108 (mtm) cc_final: 0.7901 (mtm) REVERT: D 313 MET cc_start: 0.8358 (ttt) cc_final: 0.7942 (ttt) REVERT: D 325 MET cc_start: 0.8023 (mmt) cc_final: 0.7807 (mmt) REVERT: E 100 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7636 (mt-10) REVERT: E 118 LYS cc_start: 0.8579 (mttm) cc_final: 0.8072 (mmmt) REVERT: E 123 MET cc_start: 0.8764 (mmt) cc_final: 0.8548 (mmt) REVERT: E 292 ASP cc_start: 0.7333 (m-30) cc_final: 0.7126 (m-30) REVERT: F 57 GLU cc_start: 0.8328 (pt0) cc_final: 0.8036 (pt0) REVERT: F 299 MET cc_start: 0.8766 (mtm) cc_final: 0.8554 (mtp) REVERT: G 746 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7198 (mmm) REVERT: G 863 MET cc_start: 0.7720 (mtm) cc_final: 0.6798 (ptp) REVERT: H 725 MET cc_start: 0.7749 (mtt) cc_final: 0.7359 (mtt) REVERT: H 822 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8180 (mmp) REVERT: H 863 MET cc_start: 0.8121 (mtm) cc_final: 0.7618 (mtm) REVERT: I 732 MET cc_start: 0.8281 (mtp) cc_final: 0.8017 (mtp) REVERT: K 869 GLN cc_start: 0.8795 (mm110) cc_final: 0.8505 (mm-40) REVERT: L 732 MET cc_start: 0.8189 (mtp) cc_final: 0.7969 (mtm) REVERT: L 746 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7456 (tpt) REVERT: L 794 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8341 (tp40) REVERT: Z 732 MET cc_start: 0.8243 (mtp) cc_final: 0.7921 (mtp) REVERT: Z 746 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7560 (mmm) REVERT: Z 794 GLN cc_start: 0.9079 (tp40) cc_final: 0.8828 (tp40) REVERT: Z 822 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7687 (mmm) REVERT: Z 863 MET cc_start: 0.7501 (mtm) cc_final: 0.7142 (mtm) outliers start: 36 outliers final: 7 residues processed: 335 average time/residue: 0.3632 time to fit residues: 194.7777 Evaluate side-chains 270 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 257 time to evaluate : 2.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 746 MET Chi-restraints excluded: chain H residue 822 MET Chi-restraints excluded: chain L residue 746 MET Chi-restraints excluded: chain Z residue 746 MET Chi-restraints excluded: chain Z residue 822 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.6980 chunk 236 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 chunk 159 optimal weight: 0.5980 chunk 126 optimal weight: 1.9990 chunk 244 optimal weight: 8.9990 chunk 94 optimal weight: 0.6980 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 0.6980 chunk 283 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 353 GLN K 794 GLN L 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.0963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 25296 Z= 0.175 Angle : 0.548 7.636 34242 Z= 0.275 Chirality : 0.040 0.152 3912 Planarity : 0.004 0.038 4338 Dihedral : 12.136 171.853 3511 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.86 % Allowed : 5.80 % Favored : 93.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.16), residues: 3096 helix: 1.14 (0.13), residues: 1686 sheet: -1.29 (0.27), residues: 378 loop : -0.08 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 340 HIS 0.006 0.001 HIS C 40 PHE 0.007 0.001 PHE B 127 TYR 0.011 0.001 TYR F 143 ARG 0.005 0.000 ARG E 312 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 3.735 Fit side-chains REVERT: A 118 LYS cc_start: 0.8179 (mttm) cc_final: 0.7797 (mmmt) REVERT: A 119 MET cc_start: 0.8095 (mtm) cc_final: 0.7763 (mtp) REVERT: B 66 THR cc_start: 0.9244 (p) cc_final: 0.9026 (p) REVERT: B 123 MET cc_start: 0.8590 (mmt) cc_final: 0.8300 (mmm) REVERT: B 191 LYS cc_start: 0.7604 (tttp) cc_final: 0.7254 (tttt) REVERT: B 205 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 313 MET cc_start: 0.8124 (ttt) cc_final: 0.7722 (ttt) REVERT: B 326 LYS cc_start: 0.8144 (ttpp) cc_final: 0.7921 (tttp) REVERT: B 349 LEU cc_start: 0.8501 (mt) cc_final: 0.8280 (mt) REVERT: B 372 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7454 (mtp180) REVERT: C 82 MET cc_start: 0.8416 (tpt) cc_final: 0.8190 (tpt) REVERT: C 211 ASP cc_start: 0.8494 (t0) cc_final: 0.8161 (t0) REVERT: D 191 LYS cc_start: 0.7589 (tttp) cc_final: 0.7139 (tptt) REVERT: D 311 ASP cc_start: 0.7783 (m-30) cc_final: 0.7547 (m-30) REVERT: D 313 MET cc_start: 0.8299 (ttt) cc_final: 0.7911 (ttt) REVERT: E 72 GLU cc_start: 0.7384 (tt0) cc_final: 0.7048 (tt0) REVERT: F 44 MET cc_start: 0.8419 (mtt) cc_final: 0.8181 (mtp) REVERT: F 57 GLU cc_start: 0.8347 (pt0) cc_final: 0.8031 (pt0) REVERT: F 176 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8282 (mmm) REVERT: F 283 MET cc_start: 0.8073 (mmm) cc_final: 0.7840 (mmt) REVERT: G 805 ASP cc_start: 0.7000 (m-30) cc_final: 0.6686 (m-30) REVERT: H 729 MET cc_start: 0.8428 (tpt) cc_final: 0.7596 (tpt) REVERT: H 822 MET cc_start: 0.8364 (mmm) cc_final: 0.8144 (mmm) REVERT: I 732 MET cc_start: 0.8358 (mtp) cc_final: 0.8115 (mtp) REVERT: I 822 MET cc_start: 0.8538 (mmm) cc_final: 0.7830 (mmt) REVERT: K 746 MET cc_start: 0.7819 (mmm) cc_final: 0.7333 (tpp) REVERT: K 869 GLN cc_start: 0.8838 (mm110) cc_final: 0.8518 (mm-40) REVERT: L 729 MET cc_start: 0.7541 (tpt) cc_final: 0.7310 (tpt) REVERT: L 732 MET cc_start: 0.8274 (mtm) cc_final: 0.8053 (mtm) REVERT: L 746 MET cc_start: 0.7483 (tpp) cc_final: 0.7027 (tpt) REVERT: Z 732 MET cc_start: 0.8338 (mtm) cc_final: 0.7855 (mtp) REVERT: Z 794 GLN cc_start: 0.9102 (tp40) cc_final: 0.8845 (tp40) REVERT: Z 863 MET cc_start: 0.7491 (mtm) cc_final: 0.7096 (mtm) outliers start: 23 outliers final: 18 residues processed: 296 average time/residue: 0.3738 time to fit residues: 181.6065 Evaluate side-chains 280 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 261 time to evaluate : 2.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 235 optimal weight: 0.9990 chunk 192 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 283 optimal weight: 10.0000 chunk 306 optimal weight: 3.9990 chunk 252 optimal weight: 10.0000 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 227 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 252 ASN I 837 GLN L 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 25296 Z= 0.383 Angle : 0.609 6.706 34242 Z= 0.301 Chirality : 0.045 0.166 3912 Planarity : 0.004 0.036 4338 Dihedral : 10.701 157.685 3489 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.23 % Allowed : 7.51 % Favored : 91.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.15), residues: 3096 helix: 1.06 (0.13), residues: 1680 sheet: -1.41 (0.27), residues: 366 loop : -0.18 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 340 HIS 0.005 0.001 HIS E 88 PHE 0.011 0.001 PHE C 255 TYR 0.015 0.002 TYR K 792 ARG 0.004 0.001 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 262 time to evaluate : 3.090 Fit side-chains REVERT: A 118 LYS cc_start: 0.8220 (mttm) cc_final: 0.7843 (mmmt) REVERT: A 119 MET cc_start: 0.7854 (mtm) cc_final: 0.7596 (mtp) REVERT: A 176 MET cc_start: 0.8427 (mmm) cc_final: 0.8186 (mmm) REVERT: A 369 ILE cc_start: 0.8710 (tp) cc_final: 0.8493 (tp) REVERT: B 191 LYS cc_start: 0.7777 (tttp) cc_final: 0.7353 (tttt) REVERT: B 205 GLU cc_start: 0.8235 (mt-10) cc_final: 0.7821 (mt-10) REVERT: B 305 MET cc_start: 0.8846 (mtp) cc_final: 0.8604 (mmm) REVERT: C 211 ASP cc_start: 0.8669 (t0) cc_final: 0.8337 (t0) REVERT: D 191 LYS cc_start: 0.7845 (tttp) cc_final: 0.7238 (ttmt) REVERT: D 311 ASP cc_start: 0.7841 (m-30) cc_final: 0.7590 (m-30) REVERT: D 313 MET cc_start: 0.8376 (ttt) cc_final: 0.8144 (ttt) REVERT: D 354 GLN cc_start: 0.8310 (mm-40) cc_final: 0.8014 (mm-40) REVERT: E 72 GLU cc_start: 0.7447 (tt0) cc_final: 0.7118 (tt0) REVERT: E 118 LYS cc_start: 0.8583 (mttm) cc_final: 0.8065 (mmmt) REVERT: F 57 GLU cc_start: 0.8377 (pt0) cc_final: 0.8004 (pt0) REVERT: F 61 LYS cc_start: 0.8545 (mttm) cc_final: 0.8259 (mttm) REVERT: F 325 MET cc_start: 0.8880 (mmp) cc_final: 0.8489 (mmp) REVERT: G 863 MET cc_start: 0.8505 (mtm) cc_final: 0.8075 (mtp) REVERT: H 729 MET cc_start: 0.8397 (tpt) cc_final: 0.7431 (tpt) REVERT: H 822 MET cc_start: 0.8388 (mmm) cc_final: 0.8166 (mmp) REVERT: I 822 MET cc_start: 0.8572 (mmm) cc_final: 0.8083 (mmt) REVERT: L 732 MET cc_start: 0.8308 (mtm) cc_final: 0.8096 (mtm) REVERT: L 746 MET cc_start: 0.7291 (tpp) cc_final: 0.6999 (tpt) REVERT: L 822 MET cc_start: 0.8451 (mmp) cc_final: 0.8243 (mmt) REVERT: Z 732 MET cc_start: 0.8363 (mtm) cc_final: 0.7772 (mtp) REVERT: Z 794 GLN cc_start: 0.9074 (tp40) cc_final: 0.8866 (tp40) REVERT: Z 863 MET cc_start: 0.7806 (mtm) cc_final: 0.7297 (mtm) outliers start: 33 outliers final: 29 residues processed: 286 average time/residue: 0.3338 time to fit residues: 155.7368 Evaluate side-chains 278 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 249 time to evaluate : 2.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 232 SER Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 252 ASN Chi-restraints excluded: chain E residue 300 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 833 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 0.7980 chunk 213 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 135 optimal weight: 0.8980 chunk 190 optimal weight: 0.5980 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 269 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS F 353 GLN I 837 GLN K 794 GLN L 794 GLN L 837 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 25296 Z= 0.184 Angle : 0.513 6.494 34242 Z= 0.252 Chirality : 0.040 0.145 3912 Planarity : 0.003 0.035 4338 Dihedral : 9.814 138.995 3480 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 0.89 % Allowed : 8.71 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.16), residues: 3096 helix: 1.34 (0.13), residues: 1692 sheet: -1.18 (0.28), residues: 330 loop : -0.11 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.002 0.001 HIS C 40 PHE 0.007 0.001 PHE F 31 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG K 829 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 254 time to evaluate : 2.935 Fit side-chains REVERT: A 72 GLU cc_start: 0.7355 (tt0) cc_final: 0.6916 (mt-10) REVERT: A 118 LYS cc_start: 0.8213 (mttm) cc_final: 0.7797 (mmmt) REVERT: A 119 MET cc_start: 0.7737 (mtm) cc_final: 0.7413 (mtp) REVERT: A 176 MET cc_start: 0.8464 (mmm) cc_final: 0.8249 (mmm) REVERT: A 354 GLN cc_start: 0.8408 (pt0) cc_final: 0.8182 (pt0) REVERT: A 369 ILE cc_start: 0.8704 (tp) cc_final: 0.8447 (tp) REVERT: B 176 MET cc_start: 0.7761 (mtt) cc_final: 0.7419 (mtt) REVERT: B 191 LYS cc_start: 0.7673 (tttp) cc_final: 0.7242 (tttt) REVERT: C 211 ASP cc_start: 0.8602 (t0) cc_final: 0.8255 (t0) REVERT: D 132 MET cc_start: 0.8221 (ptm) cc_final: 0.7977 (ttp) REVERT: D 311 ASP cc_start: 0.7805 (m-30) cc_final: 0.7564 (m-30) REVERT: D 313 MET cc_start: 0.8312 (ttt) cc_final: 0.8090 (ttt) REVERT: E 72 GLU cc_start: 0.7361 (tt0) cc_final: 0.6871 (tt0) REVERT: F 57 GLU cc_start: 0.8392 (pt0) cc_final: 0.8106 (pt0) REVERT: F 61 LYS cc_start: 0.8519 (mttm) cc_final: 0.8247 (mttm) REVERT: F 325 MET cc_start: 0.8839 (mmp) cc_final: 0.8608 (mmp) REVERT: G 863 MET cc_start: 0.8559 (mtm) cc_final: 0.8159 (mtp) REVERT: H 729 MET cc_start: 0.8342 (tpt) cc_final: 0.7448 (tpt) REVERT: H 822 MET cc_start: 0.8330 (mmm) cc_final: 0.8109 (mmp) REVERT: I 725 MET cc_start: 0.8202 (mtt) cc_final: 0.7703 (mtt) REVERT: I 822 MET cc_start: 0.8566 (mmm) cc_final: 0.8176 (mmt) REVERT: I 869 GLN cc_start: 0.9093 (mm110) cc_final: 0.8668 (mm110) REVERT: L 746 MET cc_start: 0.7153 (tpp) cc_final: 0.6797 (tpt) REVERT: L 822 MET cc_start: 0.8406 (mmp) cc_final: 0.8185 (mmt) REVERT: Z 732 MET cc_start: 0.8360 (mtm) cc_final: 0.8105 (mtm) REVERT: Z 863 MET cc_start: 0.7788 (mtm) cc_final: 0.7226 (mtm) outliers start: 24 outliers final: 20 residues processed: 269 average time/residue: 0.3361 time to fit residues: 149.8201 Evaluate side-chains 267 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 247 time to evaluate : 2.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 224 optimal weight: 0.7980 chunk 124 optimal weight: 1.9990 chunk 257 optimal weight: 3.9990 chunk 208 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 0.1980 chunk 270 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 360 GLN I 837 GLN L 794 GLN L 837 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25296 Z= 0.239 Angle : 0.527 6.708 34242 Z= 0.257 Chirality : 0.041 0.146 3912 Planarity : 0.003 0.033 4338 Dihedral : 9.489 138.966 3480 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.12 % Allowed : 9.41 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.16), residues: 3096 helix: 1.39 (0.13), residues: 1692 sheet: -1.17 (0.28), residues: 330 loop : -0.03 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 340 HIS 0.003 0.001 HIS E 88 PHE 0.008 0.001 PHE F 31 TYR 0.011 0.001 TYR B 143 ARG 0.002 0.000 ARG K 829 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 253 time to evaluate : 2.811 Fit side-chains REVERT: A 72 GLU cc_start: 0.7348 (tt0) cc_final: 0.6992 (mt-10) REVERT: A 118 LYS cc_start: 0.8269 (mttm) cc_final: 0.7832 (mmmt) REVERT: A 354 GLN cc_start: 0.8414 (pt0) cc_final: 0.8184 (pt0) REVERT: A 369 ILE cc_start: 0.8718 (tp) cc_final: 0.8439 (tp) REVERT: B 191 LYS cc_start: 0.7735 (tttp) cc_final: 0.7282 (tttt) REVERT: B 305 MET cc_start: 0.8771 (mtp) cc_final: 0.8534 (mmm) REVERT: C 211 ASP cc_start: 0.8623 (t0) cc_final: 0.8286 (t0) REVERT: D 132 MET cc_start: 0.8211 (ptm) cc_final: 0.7970 (ttp) REVERT: E 72 GLU cc_start: 0.7329 (tt0) cc_final: 0.6848 (tt0) REVERT: F 57 GLU cc_start: 0.8378 (pt0) cc_final: 0.8004 (pt0) REVERT: F 61 LYS cc_start: 0.8513 (mttm) cc_final: 0.8253 (mttm) REVERT: F 323 SER cc_start: 0.8956 (OUTLIER) cc_final: 0.8753 (p) REVERT: G 805 ASP cc_start: 0.6924 (m-30) cc_final: 0.6579 (m-30) REVERT: G 863 MET cc_start: 0.8692 (mtm) cc_final: 0.8333 (mtp) REVERT: H 729 MET cc_start: 0.8404 (tpt) cc_final: 0.7579 (tpt) REVERT: H 822 MET cc_start: 0.8343 (mmm) cc_final: 0.8129 (mmp) REVERT: I 729 MET cc_start: 0.8016 (tpt) cc_final: 0.7802 (tpt) REVERT: I 730 MET cc_start: 0.6682 (tpt) cc_final: 0.6469 (tpt) REVERT: I 732 MET cc_start: 0.8555 (mtm) cc_final: 0.8274 (mtp) REVERT: I 805 ASP cc_start: 0.7260 (m-30) cc_final: 0.6787 (m-30) REVERT: I 822 MET cc_start: 0.8570 (mmm) cc_final: 0.8296 (mmt) REVERT: I 869 GLN cc_start: 0.8938 (mm110) cc_final: 0.8535 (mm110) REVERT: L 729 MET cc_start: 0.7495 (tpt) cc_final: 0.7229 (tpt) REVERT: L 746 MET cc_start: 0.7090 (tpp) cc_final: 0.6716 (tpt) REVERT: Z 732 MET cc_start: 0.8347 (mtm) cc_final: 0.8011 (mtp) outliers start: 30 outliers final: 25 residues processed: 271 average time/residue: 0.3298 time to fit residues: 146.9477 Evaluate side-chains 274 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 248 time to evaluate : 2.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 2.9990 chunk 271 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 301 optimal weight: 5.9990 chunk 250 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 99 optimal weight: 0.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS I 837 GLN L 794 GLN L 837 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25296 Z= 0.248 Angle : 0.527 6.574 34242 Z= 0.256 Chirality : 0.041 0.152 3912 Planarity : 0.003 0.033 4338 Dihedral : 9.230 144.081 3480 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.08 % Allowed : 9.82 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.16), residues: 3096 helix: 1.42 (0.13), residues: 1692 sheet: -1.15 (0.28), residues: 330 loop : 0.01 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 340 HIS 0.003 0.001 HIS E 88 PHE 0.008 0.001 PHE F 31 TYR 0.011 0.001 TYR B 143 ARG 0.002 0.000 ARG K 829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 254 time to evaluate : 2.534 Fit side-chains REVERT: A 72 GLU cc_start: 0.7510 (tt0) cc_final: 0.7151 (mt-10) REVERT: A 82 MET cc_start: 0.8340 (tpt) cc_final: 0.8054 (tpt) REVERT: A 118 LYS cc_start: 0.8321 (mttm) cc_final: 0.7917 (mmmt) REVERT: A 191 LYS cc_start: 0.7985 (tttp) cc_final: 0.7468 (tttp) REVERT: A 326 LYS cc_start: 0.8533 (tttp) cc_final: 0.8192 (tttm) REVERT: A 354 GLN cc_start: 0.8430 (pt0) cc_final: 0.8203 (pt0) REVERT: A 369 ILE cc_start: 0.8709 (tp) cc_final: 0.8421 (tp) REVERT: B 191 LYS cc_start: 0.7753 (tttp) cc_final: 0.7295 (tttt) REVERT: B 305 MET cc_start: 0.8770 (mtp) cc_final: 0.8536 (mmm) REVERT: C 211 ASP cc_start: 0.8641 (t0) cc_final: 0.8295 (t0) REVERT: D 132 MET cc_start: 0.8139 (ptm) cc_final: 0.7905 (ttp) REVERT: E 72 GLU cc_start: 0.7352 (tt0) cc_final: 0.6860 (tt0) REVERT: E 325 MET cc_start: 0.8153 (mmm) cc_final: 0.7894 (mmt) REVERT: F 57 GLU cc_start: 0.8270 (pt0) cc_final: 0.7924 (pt0) REVERT: F 61 LYS cc_start: 0.8503 (mttm) cc_final: 0.8077 (mtpp) REVERT: G 795 GLN cc_start: 0.9014 (mt0) cc_final: 0.8742 (mt0) REVERT: G 805 ASP cc_start: 0.7114 (m-30) cc_final: 0.6870 (m-30) REVERT: G 863 MET cc_start: 0.8712 (mtm) cc_final: 0.8370 (mtp) REVERT: H 729 MET cc_start: 0.8408 (tpt) cc_final: 0.7639 (tpt) REVERT: H 822 MET cc_start: 0.8343 (mmm) cc_final: 0.8122 (mmp) REVERT: I 732 MET cc_start: 0.8510 (mtm) cc_final: 0.8219 (mtp) REVERT: I 805 ASP cc_start: 0.7254 (m-30) cc_final: 0.6781 (m-30) REVERT: I 822 MET cc_start: 0.8534 (mmm) cc_final: 0.7963 (mmt) REVERT: I 869 GLN cc_start: 0.8945 (mm110) cc_final: 0.8552 (mm110) REVERT: L 729 MET cc_start: 0.7384 (tpt) cc_final: 0.6847 (tpt) REVERT: L 746 MET cc_start: 0.7035 (tpp) cc_final: 0.6657 (tpt) REVERT: L 869 GLN cc_start: 0.8787 (mm110) cc_final: 0.8471 (mm110) REVERT: Z 732 MET cc_start: 0.8349 (mtm) cc_final: 0.8016 (mtp) REVERT: Z 863 MET cc_start: 0.8215 (ttm) cc_final: 0.7825 (mtp) outliers start: 29 outliers final: 24 residues processed: 271 average time/residue: 0.3319 time to fit residues: 146.5321 Evaluate side-chains 268 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 171 optimal weight: 1.9990 chunk 220 optimal weight: 2.9990 chunk 170 optimal weight: 0.9990 chunk 254 optimal weight: 0.7980 chunk 168 optimal weight: 0.6980 chunk 300 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 0.4980 chunk 138 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 40 HIS L 794 GLN Z 794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25296 Z= 0.168 Angle : 0.491 6.486 34242 Z= 0.237 Chirality : 0.040 0.172 3912 Planarity : 0.003 0.033 4338 Dihedral : 8.886 145.493 3480 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 1.08 % Allowed : 10.23 % Favored : 88.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.16), residues: 3096 helix: 1.75 (0.13), residues: 1662 sheet: -0.84 (0.27), residues: 360 loop : 0.29 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 340 HIS 0.002 0.001 HIS B 88 PHE 0.007 0.001 PHE F 31 TYR 0.010 0.001 TYR C 188 ARG 0.002 0.000 ARG A 147 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 254 time to evaluate : 3.221 Fit side-chains revert: symmetry clash REVERT: A 118 LYS cc_start: 0.8323 (mttm) cc_final: 0.7900 (mmmt) REVERT: A 191 LYS cc_start: 0.7939 (tttp) cc_final: 0.7449 (tttp) REVERT: A 326 LYS cc_start: 0.8518 (tttp) cc_final: 0.8175 (tttm) REVERT: A 354 GLN cc_start: 0.8418 (pt0) cc_final: 0.8190 (pt0) REVERT: B 191 LYS cc_start: 0.7774 (tttp) cc_final: 0.7353 (tttt) REVERT: B 305 MET cc_start: 0.8733 (mtp) cc_final: 0.8493 (mmm) REVERT: C 61 LYS cc_start: 0.8491 (mttm) cc_final: 0.8212 (mtpt) REVERT: C 145 SER cc_start: 0.9067 (t) cc_final: 0.8767 (m) REVERT: C 211 ASP cc_start: 0.8592 (t0) cc_final: 0.8251 (t0) REVERT: C 253 GLU cc_start: 0.8843 (mp0) cc_final: 0.8501 (mp0) REVERT: E 72 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.6870 (tt0) REVERT: E 325 MET cc_start: 0.8249 (OUTLIER) cc_final: 0.7604 (mmp) REVERT: F 57 GLU cc_start: 0.8255 (pt0) cc_final: 0.7958 (pt0) REVERT: F 344 SER cc_start: 0.8475 (m) cc_final: 0.8216 (p) REVERT: G 795 GLN cc_start: 0.8981 (mt0) cc_final: 0.8679 (mt0) REVERT: G 805 ASP cc_start: 0.7122 (m-30) cc_final: 0.6846 (m-30) REVERT: G 863 MET cc_start: 0.8746 (mtm) cc_final: 0.8487 (mtp) REVERT: H 729 MET cc_start: 0.8410 (tpt) cc_final: 0.7688 (tpt) REVERT: H 794 GLN cc_start: 0.8936 (tp40) cc_final: 0.8609 (tp-100) REVERT: H 822 MET cc_start: 0.8316 (mmm) cc_final: 0.8060 (mmp) REVERT: I 805 ASP cc_start: 0.7208 (m-30) cc_final: 0.6753 (m-30) REVERT: I 822 MET cc_start: 0.8510 (mmm) cc_final: 0.7945 (mmt) REVERT: I 869 GLN cc_start: 0.8945 (mm110) cc_final: 0.8561 (mm110) REVERT: L 729 MET cc_start: 0.7401 (tpt) cc_final: 0.6838 (tpt) REVERT: L 746 MET cc_start: 0.6972 (tpp) cc_final: 0.6553 (tpt) REVERT: L 869 GLN cc_start: 0.8791 (mm110) cc_final: 0.8473 (mm110) REVERT: Z 732 MET cc_start: 0.8305 (mtp) cc_final: 0.8009 (mtp) REVERT: Z 863 MET cc_start: 0.8148 (ttm) cc_final: 0.7795 (mtp) outliers start: 29 outliers final: 21 residues processed: 273 average time/residue: 0.3285 time to fit residues: 145.8150 Evaluate side-chains 272 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 249 time to evaluate : 2.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 0.0470 chunk 236 optimal weight: 3.9990 overall best weight: 1.0880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 794 GLN Z 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25296 Z= 0.224 Angle : 0.515 6.656 34242 Z= 0.249 Chirality : 0.041 0.149 3912 Planarity : 0.003 0.032 4338 Dihedral : 8.727 145.384 3480 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 1.08 % Allowed : 10.64 % Favored : 88.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.16), residues: 3096 helix: 1.56 (0.13), residues: 1698 sheet: -0.87 (0.27), residues: 360 loop : 0.18 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 340 HIS 0.004 0.001 HIS C 40 PHE 0.007 0.001 PHE C 31 TYR 0.011 0.001 TYR D 143 ARG 0.005 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 251 time to evaluate : 2.938 Fit side-chains REVERT: A 72 GLU cc_start: 0.7517 (tt0) cc_final: 0.7163 (mt-10) REVERT: A 118 LYS cc_start: 0.8328 (mttm) cc_final: 0.7904 (mmmt) REVERT: A 191 LYS cc_start: 0.7960 (tttp) cc_final: 0.7460 (tttp) REVERT: A 326 LYS cc_start: 0.8500 (tttp) cc_final: 0.8165 (tttm) REVERT: A 354 GLN cc_start: 0.8444 (pt0) cc_final: 0.8211 (pt0) REVERT: A 369 ILE cc_start: 0.8694 (tp) cc_final: 0.8395 (tp) REVERT: B 191 LYS cc_start: 0.7881 (tttp) cc_final: 0.7370 (tttt) REVERT: B 305 MET cc_start: 0.8751 (mtp) cc_final: 0.8520 (mmm) REVERT: C 61 LYS cc_start: 0.8501 (mttm) cc_final: 0.8221 (mtpt) REVERT: C 211 ASP cc_start: 0.8629 (t0) cc_final: 0.8307 (t0) REVERT: E 72 GLU cc_start: 0.7474 (OUTLIER) cc_final: 0.7001 (tt0) REVERT: F 57 GLU cc_start: 0.8284 (pt0) cc_final: 0.7996 (pt0) REVERT: G 795 GLN cc_start: 0.8994 (mt0) cc_final: 0.8696 (mt0) REVERT: G 863 MET cc_start: 0.8758 (mtm) cc_final: 0.8383 (mtm) REVERT: H 729 MET cc_start: 0.8405 (tpt) cc_final: 0.7710 (tpt) REVERT: H 822 MET cc_start: 0.8314 (mmm) cc_final: 0.8081 (mmp) REVERT: I 725 MET cc_start: 0.8187 (mmm) cc_final: 0.7703 (mtt) REVERT: I 732 MET cc_start: 0.8448 (mtm) cc_final: 0.8226 (mtp) REVERT: I 805 ASP cc_start: 0.7208 (m-30) cc_final: 0.6776 (m-30) REVERT: I 822 MET cc_start: 0.8508 (mmm) cc_final: 0.7975 (mmt) REVERT: I 869 GLN cc_start: 0.8949 (mm110) cc_final: 0.8558 (mm110) REVERT: L 729 MET cc_start: 0.7394 (tpt) cc_final: 0.6846 (tpt) REVERT: L 746 MET cc_start: 0.6938 (tpp) cc_final: 0.6527 (tpt) REVERT: L 869 GLN cc_start: 0.8796 (mm110) cc_final: 0.8476 (mm110) REVERT: Z 732 MET cc_start: 0.8316 (mtp) cc_final: 0.7972 (mtp) REVERT: Z 863 MET cc_start: 0.8154 (ttm) cc_final: 0.7801 (mtp) outliers start: 29 outliers final: 24 residues processed: 272 average time/residue: 0.3384 time to fit residues: 148.8224 Evaluate side-chains 272 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 247 time to evaluate : 2.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.8980 chunk 288 optimal weight: 4.9990 chunk 262 optimal weight: 0.7980 chunk 280 optimal weight: 1.9990 chunk 168 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 220 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 253 optimal weight: 10.0000 chunk 265 optimal weight: 3.9990 chunk 279 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 25296 Z= 0.260 Angle : 0.529 6.998 34242 Z= 0.256 Chirality : 0.042 0.165 3912 Planarity : 0.003 0.032 4338 Dihedral : 8.642 147.959 3480 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.00 % Allowed : 10.68 % Favored : 88.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.16), residues: 3096 helix: 1.52 (0.13), residues: 1698 sheet: -1.09 (0.28), residues: 330 loop : 0.11 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 340 HIS 0.004 0.001 HIS C 40 PHE 0.008 0.001 PHE C 31 TYR 0.012 0.001 TYR D 143 ARG 0.002 0.000 ARG D 290 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 249 time to evaluate : 2.713 Fit side-chains REVERT: A 72 GLU cc_start: 0.7534 (tt0) cc_final: 0.7192 (mt-10) REVERT: A 118 LYS cc_start: 0.8328 (mttm) cc_final: 0.7909 (mmmt) REVERT: A 191 LYS cc_start: 0.7981 (tttp) cc_final: 0.7478 (tttp) REVERT: A 326 LYS cc_start: 0.8485 (tttp) cc_final: 0.8153 (tttm) REVERT: A 354 GLN cc_start: 0.8452 (pt0) cc_final: 0.8216 (pt0) REVERT: A 369 ILE cc_start: 0.8683 (tp) cc_final: 0.8395 (tp) REVERT: B 191 LYS cc_start: 0.7742 (tttp) cc_final: 0.7217 (tttt) REVERT: B 305 MET cc_start: 0.8763 (mtp) cc_final: 0.8528 (mmm) REVERT: C 61 LYS cc_start: 0.8497 (mttm) cc_final: 0.8219 (mtpt) REVERT: C 211 ASP cc_start: 0.8659 (t0) cc_final: 0.8308 (t0) REVERT: E 72 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7088 (tt0) REVERT: F 57 GLU cc_start: 0.8275 (pt0) cc_final: 0.7973 (pt0) REVERT: F 61 LYS cc_start: 0.8461 (mttm) cc_final: 0.8058 (mtpp) REVERT: F 227 MET cc_start: 0.8195 (mmt) cc_final: 0.7587 (mmm) REVERT: F 299 MET cc_start: 0.9062 (mmm) cc_final: 0.8612 (mtt) REVERT: G 795 GLN cc_start: 0.9012 (mt0) cc_final: 0.8734 (mt0) REVERT: G 863 MET cc_start: 0.8771 (mtm) cc_final: 0.8503 (mtm) REVERT: H 729 MET cc_start: 0.8415 (tpt) cc_final: 0.7729 (tpt) REVERT: H 822 MET cc_start: 0.8323 (mmm) cc_final: 0.8084 (mmp) REVERT: I 732 MET cc_start: 0.8482 (mtm) cc_final: 0.8281 (mtp) REVERT: I 805 ASP cc_start: 0.7219 (m-30) cc_final: 0.6779 (m-30) REVERT: I 822 MET cc_start: 0.8503 (mmm) cc_final: 0.7992 (mmt) REVERT: I 869 GLN cc_start: 0.8955 (mm110) cc_final: 0.8563 (mm110) REVERT: L 746 MET cc_start: 0.6929 (tpp) cc_final: 0.6505 (tpt) REVERT: L 869 GLN cc_start: 0.8791 (mm110) cc_final: 0.8474 (mm110) REVERT: Z 732 MET cc_start: 0.8327 (mtp) cc_final: 0.7999 (mtp) REVERT: Z 863 MET cc_start: 0.8176 (ttm) cc_final: 0.7855 (mtp) outliers start: 27 outliers final: 25 residues processed: 268 average time/residue: 0.3368 time to fit residues: 146.1100 Evaluate side-chains 270 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 244 time to evaluate : 2.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 57 GLU Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 1.9990 chunk 180 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 chunk 205 optimal weight: 1.9990 chunk 310 optimal weight: 2.9990 chunk 286 optimal weight: 8.9990 chunk 247 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 191 optimal weight: 0.6980 chunk 151 optimal weight: 0.0670 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 794 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25296 Z= 0.197 Angle : 0.507 6.751 34242 Z= 0.244 Chirality : 0.040 0.159 3912 Planarity : 0.003 0.032 4338 Dihedral : 8.519 151.530 3480 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.00 % Allowed : 10.83 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.16), residues: 3096 helix: 1.61 (0.13), residues: 1698 sheet: -0.81 (0.27), residues: 360 loop : 0.18 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 340 HIS 0.005 0.001 HIS C 40 PHE 0.007 0.001 PHE F 31 TYR 0.010 0.001 TYR D 143 ARG 0.003 0.000 ARG B 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 241 time to evaluate : 2.726 Fit side-chains REVERT: A 72 GLU cc_start: 0.7505 (tt0) cc_final: 0.7171 (mt-10) REVERT: A 118 LYS cc_start: 0.8328 (mttm) cc_final: 0.7901 (mmmt) REVERT: A 191 LYS cc_start: 0.7963 (tttp) cc_final: 0.7462 (tttp) REVERT: A 326 LYS cc_start: 0.8481 (tttp) cc_final: 0.8159 (tttm) REVERT: A 354 GLN cc_start: 0.8456 (pt0) cc_final: 0.8226 (pt0) REVERT: B 191 LYS cc_start: 0.7793 (tttp) cc_final: 0.7296 (tttt) REVERT: B 305 MET cc_start: 0.8740 (mtp) cc_final: 0.8504 (mmm) REVERT: C 61 LYS cc_start: 0.8485 (mttm) cc_final: 0.8194 (mtpt) REVERT: C 211 ASP cc_start: 0.8615 (t0) cc_final: 0.8282 (t0) REVERT: E 72 GLU cc_start: 0.7509 (tt0) cc_final: 0.7070 (tt0) REVERT: F 57 GLU cc_start: 0.8267 (pt0) cc_final: 0.7981 (pt0) REVERT: F 227 MET cc_start: 0.8160 (mmt) cc_final: 0.7484 (mmm) REVERT: G 795 GLN cc_start: 0.8991 (mt0) cc_final: 0.8701 (mt0) REVERT: G 805 ASP cc_start: 0.6989 (m-30) cc_final: 0.6575 (m-30) REVERT: G 863 MET cc_start: 0.8768 (mtm) cc_final: 0.8533 (mtm) REVERT: H 729 MET cc_start: 0.8442 (tpt) cc_final: 0.7795 (tpt) REVERT: H 794 GLN cc_start: 0.8957 (tp40) cc_final: 0.8613 (tp-100) REVERT: H 822 MET cc_start: 0.8312 (mmm) cc_final: 0.8066 (mmp) REVERT: I 725 MET cc_start: 0.7818 (mtt) cc_final: 0.6858 (mtt) REVERT: I 732 MET cc_start: 0.8456 (mtm) cc_final: 0.8255 (mtp) REVERT: I 805 ASP cc_start: 0.7108 (m-30) cc_final: 0.6660 (m-30) REVERT: I 822 MET cc_start: 0.8492 (mmm) cc_final: 0.7984 (mmt) REVERT: I 869 GLN cc_start: 0.8947 (mm110) cc_final: 0.8568 (mm110) REVERT: K 822 MET cc_start: 0.8172 (tpp) cc_final: 0.7864 (mmt) REVERT: L 729 MET cc_start: 0.7552 (tpt) cc_final: 0.7325 (tpt) REVERT: L 746 MET cc_start: 0.6901 (tpp) cc_final: 0.6463 (tpt) REVERT: L 869 GLN cc_start: 0.8800 (mm110) cc_final: 0.8486 (mm110) REVERT: Z 732 MET cc_start: 0.8329 (mtp) cc_final: 0.7986 (mtp) REVERT: Z 863 MET cc_start: 0.8172 (ttm) cc_final: 0.7860 (mtp) outliers start: 27 outliers final: 22 residues processed: 259 average time/residue: 0.3386 time to fit residues: 142.4679 Evaluate side-chains 262 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 240 time to evaluate : 2.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 283 MET Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 99 GLU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 199 SER Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 3.9990 chunk 263 optimal weight: 0.7980 chunk 75 optimal weight: 0.0270 chunk 228 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 68 optimal weight: 0.0060 chunk 247 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.9456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 794 GLN Z 794 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.109289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.088941 restraints weight = 27375.936| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 0.96 r_work: 0.2710 rms_B_bonded: 1.30 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 2.24 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25296 Z= 0.203 Angle : 0.506 6.777 34242 Z= 0.243 Chirality : 0.040 0.153 3912 Planarity : 0.003 0.033 4338 Dihedral : 8.423 160.239 3480 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.97 % Allowed : 11.01 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.16), residues: 3096 helix: 1.76 (0.13), residues: 1668 sheet: -0.80 (0.27), residues: 360 loop : 0.36 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 340 HIS 0.004 0.001 HIS C 40 PHE 0.007 0.001 PHE F 31 TYR 0.011 0.001 TYR D 143 ARG 0.003 0.000 ARG B 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4498.28 seconds wall clock time: 82 minutes 14.57 seconds (4934.57 seconds total)