Starting phenix.real_space_refine on Fri Sep 27 11:35:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/09_2024/7ad9_11721.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/09_2024/7ad9_11721.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/09_2024/7ad9_11721.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/09_2024/7ad9_11721.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/09_2024/7ad9_11721.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ad9_11721/09_2024/7ad9_11721.cif" } resolution = 3.5 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= 0.002 sd= 0.009 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 15 5.49 5 Mg 5 5.21 5 S 115 5.16 5 C 9810 2.51 5 N 2605 2.21 5 O 3010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 15560 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "B" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "D" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "L" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "H" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "F" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 124 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "I" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} 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: "O" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "P" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "P" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "Q" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "Q" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "R" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "R" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "S" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 42 Classifications: {'peptide': 5} Link IDs: {'TRANS': 4} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'EEP:plan-1': 1, 'HYP:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "S" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 13 Classifications: {'peptide': 2} Modifications used: {'DTH_chir_02_both': 1, 'PEPT-D': 1} Link IDs: {'TRANS': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.84, per 1000 atoms: 0.63 Number of scatterers: 15560 At special positions: 0 Unit cell: (99.22, 91.96, 191.18, 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 115 16.00 P 15 15.00 Mg 5 11.99 O 3010 8.00 N 2605 7.00 C 9810 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=5, symmetry=0 Links applied TRANS " DTH O 6 " - " ALA O 5 " " DTH P 6 " - " ALA P 5 " " DTH Q 6 " - " ALA Q 5 " " DTH R 6 " - " ALA R 5 " " DTH S 6 " - " ALA S 5 " Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.51 Conformation dependent library (CDL) restraints added in 2.0 seconds 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input residue name is d-peptide pdb=" CB DTH O 6 " pdb=" CB DTH P 6 " pdb=" CB DTH Q 6 " pdb=" CB DTH R 6 " pdb=" CB DTH S 6 " Number of C-beta restraints generated: 3640 Finding SS restraints... Secondary structure from input PDB file: 130 helices and 30 sheets defined 54.2% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 2 through 16 Processing helix chain 'B' and resid 44 through 48 Processing helix chain 'B' and resid 55 through 60 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 78 through 92 Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.078A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 144 removed outlier: 3.775A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 175 Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 194 through 197 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 257 Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 268 Processing helix chain 'B' and resid 273 through 284 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 Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.613A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 318 Processing helix chain 'B' and resid 332 through 336 removed outlier: 3.536A pdb=" N ARG B 335 " --> pdb=" O PRO B 332 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS B 336 " --> pdb=" O PRO B 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 332 through 336' Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 348 through 353 removed outlier: 6.222A pdb=" N THR B 351 " --> pdb=" O SER B 348 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.531A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 372 Processing helix chain 'C' and resid 2 through 16 Processing helix chain 'D' and resid 44 through 48 Processing helix chain 'D' and resid 55 through 60 Processing helix chain 'D' and resid 61 through 65 Processing helix chain 'D' and resid 78 through 92 Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.077A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 144 removed outlier: 3.774A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 175 Processing helix chain 'D' and resid 181 through 193 Processing helix chain 'D' and resid 194 through 197 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 252 through 257 Processing helix chain 'D' and resid 258 through 262 Processing helix chain 'D' and resid 263 through 268 Processing helix chain 'D' and resid 273 through 284 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 Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.613A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 318 Processing helix chain 'D' and resid 332 through 336 removed outlier: 3.536A pdb=" N ARG D 335 " --> pdb=" O PRO D 332 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS D 336 " --> pdb=" O PRO D 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 332 through 336' Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 348 through 353 removed outlier: 6.223A pdb=" N THR D 351 " --> pdb=" O SER D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.531A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 367 through 372 Processing helix chain 'L' and resid 2 through 16 Processing helix chain 'H' and resid 44 through 48 Processing helix chain 'H' and resid 55 through 60 Processing helix chain 'H' and resid 61 through 65 Processing helix chain 'H' and resid 78 through 92 Processing helix chain 'H' and resid 97 through 101 Processing helix chain 'H' and resid 112 through 126 removed outlier: 4.077A pdb=" N ARG H 116 " --> pdb=" O PRO H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 137 through 144 removed outlier: 3.775A pdb=" N LEU H 142 " --> pdb=" O ALA H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 175 Processing helix chain 'H' and resid 181 through 193 Processing helix chain 'H' and resid 194 through 197 Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 222 through 231 Processing helix chain 'H' and resid 252 through 257 Processing helix chain 'H' and resid 258 through 262 Processing helix chain 'H' and resid 263 through 268 Processing helix chain 'H' and resid 273 through 284 Processing helix chain 'H' and resid 286 through 288 No H-bonds generated for 'chain 'H' and resid 286 through 288' Processing helix chain 'H' and resid 289 through 295 Processing helix chain 'H' and resid 301 through 306 removed outlier: 3.612A pdb=" N TYR H 306 " --> pdb=" O THR H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 318 Processing helix chain 'H' and resid 332 through 336 removed outlier: 3.536A pdb=" N ARG H 335 " --> pdb=" O PRO H 332 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS H 336 " --> pdb=" O PRO H 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 332 through 336' Processing helix chain 'H' and resid 337 through 347 Processing helix chain 'H' and resid 348 through 353 removed outlier: 6.223A pdb=" N THR H 351 " --> pdb=" O SER H 348 " (cutoff:3.500A) Processing helix chain 'H' and resid 359 through 366 removed outlier: 3.530A pdb=" N GLU H 364 " --> pdb=" O GLN H 360 " (cutoff:3.500A) Processing helix chain 'H' and resid 367 through 372 Processing helix chain 'E' and resid 2 through 16 Processing helix chain 'F' and resid 44 through 48 Processing helix chain 'F' and resid 55 through 60 Processing helix chain 'F' and resid 61 through 65 Processing helix chain 'F' and resid 78 through 92 Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.078A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 144 removed outlier: 3.775A pdb=" N LEU F 142 " --> pdb=" O ALA F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 175 Processing helix chain 'F' and resid 181 through 193 Processing helix chain 'F' and resid 194 through 197 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 231 Processing helix chain 'F' and resid 252 through 257 Processing helix chain 'F' and resid 258 through 262 Processing helix chain 'F' and resid 263 through 268 Processing helix chain 'F' and resid 273 through 284 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 Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.613A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 318 Processing helix chain 'F' and resid 332 through 336 removed outlier: 3.537A pdb=" N ARG F 335 " --> pdb=" O PRO F 332 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N LYS F 336 " --> pdb=" O PRO F 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 332 through 336' Processing helix chain 'F' and resid 337 through 347 Processing helix chain 'F' and resid 348 through 353 removed outlier: 6.222A pdb=" N THR F 351 " --> pdb=" O SER F 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 removed outlier: 3.531A pdb=" N GLU F 364 " --> pdb=" O GLN F 360 " (cutoff:3.500A) Processing helix chain 'F' and resid 367 through 372 Processing helix chain 'G' and resid 2 through 16 Processing helix chain 'I' and resid 44 through 48 Processing helix chain 'I' and resid 55 through 60 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'I' and resid 78 through 92 Processing helix chain 'I' and resid 97 through 101 Processing helix chain 'I' and resid 112 through 126 removed outlier: 4.078A pdb=" N ARG I 116 " --> pdb=" O PRO I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 137 through 144 removed outlier: 3.775A pdb=" N LEU I 142 " --> pdb=" O ALA I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 172 through 175 Processing helix chain 'I' and resid 181 through 193 Processing helix chain 'I' and resid 194 through 197 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 222 through 231 Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 258 through 262 Processing helix chain 'I' and resid 263 through 268 Processing helix chain 'I' and resid 273 through 284 Processing helix chain 'I' and resid 286 through 288 No H-bonds generated for 'chain 'I' and resid 286 through 288' Processing helix chain 'I' and resid 289 through 295 Processing helix chain 'I' and resid 301 through 306 removed outlier: 3.612A pdb=" N TYR I 306 " --> pdb=" O THR I 303 " (cutoff:3.500A) Processing helix chain 'I' and resid 308 through 318 Processing helix chain 'I' and resid 332 through 336 removed outlier: 3.536A pdb=" N ARG I 335 " --> pdb=" O PRO I 332 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LYS I 336 " --> pdb=" O PRO I 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 332 through 336' Processing helix chain 'I' and resid 337 through 347 Processing helix chain 'I' and resid 348 through 353 removed outlier: 6.223A pdb=" N THR I 351 " --> pdb=" O SER I 348 " (cutoff:3.500A) Processing helix chain 'I' and resid 359 through 366 removed outlier: 3.531A pdb=" N GLU I 364 " --> pdb=" O GLN I 360 " (cutoff:3.500A) Processing helix chain 'I' and resid 367 through 372 Processing sheet with id=AA1, first strand: chain 'B' and resid 17 through 21 removed outlier: 6.661A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA5, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.467A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 21 removed outlier: 6.660A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AB1, first strand: chain 'D' and resid 169 through 170 Processing sheet with id=AB2, first strand: chain 'D' and resid 169 through 170 removed outlier: 6.468A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'H' and resid 17 through 21 removed outlier: 6.660A pdb=" N LEU H 8 " --> pdb=" O LEU H 104 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR H 106 " --> pdb=" O LEU H 8 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N CYS H 10 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR H 103 " --> pdb=" O TYR H 133 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N ALA H 135 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N LEU H 105 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'H' and resid 71 through 72 Processing sheet with id=AB7, first strand: chain 'H' and resid 169 through 170 Processing sheet with id=AB8, first strand: chain 'H' and resid 169 through 170 removed outlier: 6.469A pdb=" N ASN H 297 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 238 through 241 Processing sheet with id=AC1, first strand: chain 'F' and resid 17 through 21 removed outlier: 6.660A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.551A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.694A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AC3, first strand: chain 'F' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'F' and resid 169 through 170 Processing sheet with id=AC5, first strand: chain 'F' and resid 169 through 170 removed outlier: 6.468A pdb=" N ASN F 297 " --> pdb=" O ILE F 330 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AC7, first strand: chain 'I' and resid 17 through 21 removed outlier: 6.661A pdb=" N LEU I 8 " --> pdb=" O LEU I 104 " (cutoff:3.500A) removed outlier: 8.550A pdb=" N THR I 106 " --> pdb=" O LEU I 8 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N CYS I 10 " --> pdb=" O THR I 106 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N THR I 103 " --> pdb=" O TYR I 133 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ALA I 135 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N LEU I 105 " --> pdb=" O ALA I 135 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 35 through 36 Processing sheet with id=AC9, first strand: chain 'I' and resid 71 through 72 Processing sheet with id=AD1, first strand: chain 'I' and resid 169 through 170 Processing sheet with id=AD2, first strand: chain 'I' and resid 169 through 170 removed outlier: 6.468A pdb=" N ASN I 297 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 238 through 241 730 hydrogen bonds defined for protein. 1755 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.69 Time building geometry restraints manager: 5.16 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: 4914 1.34 - 1.46: 3552 1.46 - 1.58: 7199 1.58 - 1.70: 15 1.70 - 1.82: 200 Bond restraints: 15880 Sorted by residual: bond pdb=" CA ILE D 151 " pdb=" C ILE D 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.49e+01 bond pdb=" CA ILE F 151 " pdb=" C ILE F 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.46e+01 bond pdb=" CA ILE H 151 " pdb=" C ILE H 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.45e+01 bond pdb=" CA ILE I 151 " pdb=" C ILE I 151 " ideal model delta sigma weight residual 1.522 1.463 0.059 1.19e-02 7.06e+03 2.44e+01 bond pdb=" CA ILE B 151 " pdb=" C ILE B 151 " ideal model delta sigma weight residual 1.522 1.464 0.058 1.19e-02 7.06e+03 2.41e+01 ... (remaining 15875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 18223 2.03 - 4.05: 2671 4.05 - 6.08: 492 6.08 - 8.10: 106 8.10 - 10.13: 38 Bond angle restraints: 21530 Sorted by residual: angle pdb=" N VAL F 54 " pdb=" CA VAL F 54 " pdb=" C VAL F 54 " ideal model delta sigma weight residual 108.12 115.88 -7.76 1.44e+00 4.82e-01 2.91e+01 angle pdb=" N VAL B 54 " pdb=" CA VAL B 54 " pdb=" C VAL B 54 " ideal model delta sigma weight residual 108.12 115.86 -7.74 1.44e+00 4.82e-01 2.89e+01 angle pdb=" N VAL I 54 " pdb=" CA VAL I 54 " pdb=" C VAL I 54 " ideal model delta sigma weight residual 108.12 115.85 -7.73 1.44e+00 4.82e-01 2.88e+01 angle pdb=" N VAL D 54 " pdb=" CA VAL D 54 " pdb=" C VAL D 54 " ideal model delta sigma weight residual 108.12 115.84 -7.72 1.44e+00 4.82e-01 2.87e+01 angle pdb=" N VAL H 54 " pdb=" CA VAL H 54 " pdb=" C VAL H 54 " ideal model delta sigma weight residual 108.12 115.84 -7.72 1.44e+00 4.82e-01 2.87e+01 ... (remaining 21525 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.01: 9335 29.01 - 58.02: 195 58.02 - 87.02: 20 87.02 - 116.03: 5 116.03 - 145.04: 10 Dihedral angle restraints: 9565 sinusoidal: 3890 harmonic: 5675 Sorted by residual: dihedral pdb=" O1B ADP D 401 " pdb=" O3A ADP D 401 " pdb=" PB ADP D 401 " pdb=" PA ADP D 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.04 -145.04 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP F 401 " pdb=" O3A ADP F 401 " pdb=" PB ADP F 401 " pdb=" PA ADP F 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.02 -145.02 1 2.00e+01 2.50e-03 4.37e+01 dihedral pdb=" O1B ADP H 401 " pdb=" O3A ADP H 401 " pdb=" PB ADP H 401 " pdb=" PA ADP H 401 " ideal model delta sinusoidal sigma weight residual -60.00 85.01 -145.01 1 2.00e+01 2.50e-03 4.37e+01 ... (remaining 9562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1303 0.057 - 0.115: 760 0.115 - 0.172: 218 0.172 - 0.230: 80 0.230 - 0.287: 39 Chirality restraints: 2400 Sorted by residual: chirality pdb=" CB ILE D 151 " pdb=" CA ILE D 151 " pdb=" CG1 ILE D 151 " pdb=" CG2 ILE D 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CB ILE I 151 " pdb=" CA ILE I 151 " pdb=" CG1 ILE I 151 " pdb=" CG2 ILE I 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CB ILE H 151 " pdb=" CA ILE H 151 " pdb=" CG1 ILE H 151 " pdb=" CG2 ILE H 151 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.05e+00 ... (remaining 2397 not shown) Planarity restraints: 2725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 11 " -0.028 2.00e-02 2.50e+03 5.73e-02 3.29e+01 pdb=" CG ASP D 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP D 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP D 11 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP I 11 " -0.028 2.00e-02 2.50e+03 5.73e-02 3.28e+01 pdb=" CG ASP I 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP I 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP I 11 " -0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP H 11 " -0.028 2.00e-02 2.50e+03 5.71e-02 3.26e+01 pdb=" CG ASP H 11 " 0.099 2.00e-02 2.50e+03 pdb=" OD1 ASP H 11 " -0.036 2.00e-02 2.50e+03 pdb=" OD2 ASP H 11 " -0.034 2.00e-02 2.50e+03 ... (remaining 2722 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.39: 30 2.39 - 3.02: 9825 3.02 - 3.65: 23068 3.65 - 4.27: 38920 4.27 - 4.90: 61432 Nonbonded interactions: 133275 Sorted by model distance: nonbonded pdb=" CD1 TRP R 3 " pdb=" SG CYS R 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP P 3 " pdb=" SG CYS P 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP S 3 " pdb=" SG CYS S 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP O 3 " pdb=" SG CYS O 7 " model vdw 1.765 3.620 nonbonded pdb=" CD1 TRP Q 3 " pdb=" SG CYS Q 7 " model vdw 1.766 3.620 ... (remaining 133270 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 'C' selection = chain 'E' selection = chain 'G' selection = chain 'L' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'I' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.590 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 39.000 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 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 : 0.017 0.093 15880 Z= 1.083 Angle : 1.607 10.129 21530 Z= 0.979 Chirality : 0.082 0.287 2400 Planarity : 0.011 0.057 2720 Dihedral : 12.965 145.040 5910 Min Nonbonded Distance : 1.765 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.30 % Allowed : 0.30 % Favored : 99.39 % Cbeta Deviations : 0.27 % 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: -0.26 (0.19), residues: 1900 helix: -1.30 (0.15), residues: 880 sheet: 0.22 (0.33), residues: 225 loop : 1.47 (0.23), residues: 795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.005 TRP H 340 HIS 0.031 0.007 HIS F 40 PHE 0.053 0.008 PHE B 124 TYR 0.063 0.007 TYR B 143 ARG 0.020 0.004 ARG I 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 443 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 438 time to evaluate : 1.730 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 78 ASN cc_start: 0.7662 (t0) cc_final: 0.6847 (t0) REVERT: B 82 MET cc_start: 0.9072 (tpt) cc_final: 0.8852 (tpt) REVERT: B 190 MET cc_start: 0.7943 (mtp) cc_final: 0.7630 (mtp) REVERT: B 305 MET cc_start: 0.8823 (mmm) cc_final: 0.8482 (mmt) REVERT: B 326 LYS cc_start: 0.8131 (tptt) cc_final: 0.7749 (tttt) REVERT: D 113 LYS cc_start: 0.7920 (mttt) cc_final: 0.7673 (mtmt) REVERT: D 115 ASN cc_start: 0.8415 (t0) cc_final: 0.8187 (t0) REVERT: D 119 MET cc_start: 0.8350 (ttp) cc_final: 0.8139 (ttm) REVERT: D 151 ILE cc_start: 0.8854 (mt) cc_final: 0.8583 (mt) REVERT: H 44 MET cc_start: 0.7546 (mtp) cc_final: 0.7341 (mtm) REVERT: H 115 ASN cc_start: 0.8445 (t0) cc_final: 0.8082 (m-40) REVERT: F 305 MET cc_start: 0.8620 (mmm) cc_final: 0.8213 (mmt) REVERT: I 154 ASP cc_start: 0.8289 (t0) cc_final: 0.7895 (t70) REVERT: I 225 ASN cc_start: 0.8338 (m-40) cc_final: 0.7865 (m110) REVERT: I 274 ILE cc_start: 0.8022 (pt) cc_final: 0.7808 (tt) REVERT: I 283 MET cc_start: 0.8566 (mmp) cc_final: 0.8354 (mmt) outliers start: 5 outliers final: 0 residues processed: 441 average time/residue: 0.2906 time to fit residues: 182.7067 Evaluate side-chains 202 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.9990 chunk 144 optimal weight: 0.7980 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 148 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 172 optimal weight: 3.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 HIS ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 115 ASN D 40 HIS D 246 GLN H 40 HIS H 121 GLN H 353 GLN F 12 ASN F 49 GLN F 121 GLN I 128 ASN I 314 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15880 Z= 0.215 Angle : 0.648 8.114 21530 Z= 0.323 Chirality : 0.047 0.182 2400 Planarity : 0.004 0.049 2720 Dihedral : 11.153 114.648 2245 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.61 % Allowed : 7.54 % Favored : 89.85 % 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: 0.89 (0.19), residues: 1900 helix: 0.26 (0.17), residues: 840 sheet: 0.34 (0.34), residues: 235 loop : 1.36 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 340 HIS 0.006 0.001 HIS B 101 PHE 0.034 0.002 PHE D 375 TYR 0.016 0.001 TYR H 294 ARG 0.007 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 245 time to evaluate : 1.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 123 MET cc_start: 0.7258 (mmm) cc_final: 0.6913 (mmm) REVERT: B 325 MET cc_start: 0.6736 (mtm) cc_final: 0.6373 (mtt) REVERT: B 326 LYS cc_start: 0.8107 (tptt) cc_final: 0.7849 (tttt) REVERT: D 119 MET cc_start: 0.8256 (ttp) cc_final: 0.8009 (ttm) REVERT: L 11 GLU cc_start: 0.7690 (tp30) cc_final: 0.7428 (tp30) REVERT: H 115 ASN cc_start: 0.8175 (t0) cc_final: 0.7860 (m-40) REVERT: H 128 ASN cc_start: 0.7774 (m-40) cc_final: 0.7356 (t0) REVERT: H 206 ARG cc_start: 0.8040 (OUTLIER) cc_final: 0.6726 (ttp80) REVERT: F 176 MET cc_start: 0.7902 (mmm) cc_final: 0.7688 (mmt) REVERT: F 337 TYR cc_start: 0.7535 (m-80) cc_final: 0.7258 (m-80) REVERT: F 344 SER cc_start: 0.9280 (OUTLIER) cc_final: 0.8735 (m) REVERT: G 1 MET cc_start: 0.6048 (ptt) cc_final: 0.4894 (ptm) REVERT: G 9 LYS cc_start: 0.7743 (OUTLIER) cc_final: 0.7250 (ttpp) REVERT: I 12 ASN cc_start: 0.7352 (m110) cc_final: 0.6800 (p0) REVERT: I 95 ARG cc_start: 0.7668 (mmm160) cc_final: 0.6967 (mmt180) REVERT: I 154 ASP cc_start: 0.8138 (t0) cc_final: 0.7738 (t70) REVERT: I 178 LEU cc_start: 0.8778 (mt) cc_final: 0.8566 (mt) REVERT: I 225 ASN cc_start: 0.8317 (m-40) cc_final: 0.7731 (m110) REVERT: I 289 ILE cc_start: 0.8453 (mm) cc_final: 0.8196 (mm) outliers start: 43 outliers final: 16 residues processed: 275 average time/residue: 0.2619 time to fit residues: 107.5333 Evaluate side-chains 205 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 186 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 5 ASP Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 372 ARG Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain H residue 206 ARG Chi-restraints excluded: chain F residue 56 ASP Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain I residue 6 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 95 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 172 optimal weight: 0.8980 chunk 186 optimal weight: 3.9990 chunk 153 optimal weight: 3.9990 chunk 171 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 12 ASN H 297 ASN F 115 ASN I 115 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15880 Z= 0.185 Angle : 0.586 8.299 21530 Z= 0.285 Chirality : 0.045 0.159 2400 Planarity : 0.004 0.059 2720 Dihedral : 9.545 99.538 2245 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.01 % Allowed : 10.15 % Favored : 87.84 % 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: 1.10 (0.19), residues: 1900 helix: 0.50 (0.18), residues: 875 sheet: 0.50 (0.35), residues: 225 loop : 1.39 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 340 HIS 0.004 0.001 HIS F 371 PHE 0.019 0.002 PHE D 375 TYR 0.013 0.001 TYR I 294 ARG 0.005 0.000 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 213 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: B 8 LEU cc_start: 0.9167 (OUTLIER) cc_final: 0.8966 (tt) REVERT: B 325 MET cc_start: 0.6548 (mtm) cc_final: 0.6274 (mtt) REVERT: B 326 LYS cc_start: 0.8171 (tptt) cc_final: 0.7911 (tttt) REVERT: D 119 MET cc_start: 0.8214 (ttp) cc_final: 0.7870 (ttm) REVERT: H 115 ASN cc_start: 0.8474 (t0) cc_final: 0.7806 (m-40) REVERT: E 8 LYS cc_start: 0.8076 (OUTLIER) cc_final: 0.7836 (mtmt) REVERT: F 176 MET cc_start: 0.7963 (mmm) cc_final: 0.7691 (mmt) REVERT: F 289 ILE cc_start: 0.8725 (mm) cc_final: 0.8524 (mm) REVERT: F 313 MET cc_start: 0.8660 (tpp) cc_final: 0.8448 (ttm) REVERT: F 337 TYR cc_start: 0.7475 (m-80) cc_final: 0.6978 (m-80) REVERT: F 344 SER cc_start: 0.9349 (OUTLIER) cc_final: 0.8746 (m) REVERT: G 9 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7313 (ttmm) REVERT: I 78 ASN cc_start: 0.6081 (t0) cc_final: 0.5208 (t0) REVERT: I 81 ASP cc_start: 0.7209 (m-30) cc_final: 0.6929 (m-30) REVERT: I 95 ARG cc_start: 0.7725 (mmm160) cc_final: 0.7208 (mmt180) REVERT: I 154 ASP cc_start: 0.8156 (t0) cc_final: 0.7774 (t70) REVERT: I 289 ILE cc_start: 0.8532 (mm) cc_final: 0.8249 (mm) outliers start: 33 outliers final: 17 residues processed: 235 average time/residue: 0.2575 time to fit residues: 91.0316 Evaluate side-chains 202 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 181 time to evaluate : 1.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain F residue 344 SER Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 115 ASN Chi-restraints excluded: chain I residue 194 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 170 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 173 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 90 optimal weight: 0.0060 chunk 164 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 297 ASN I 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.4326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15880 Z= 0.186 Angle : 0.567 7.664 21530 Z= 0.273 Chirality : 0.045 0.160 2400 Planarity : 0.004 0.059 2720 Dihedral : 8.639 94.253 2245 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.19 % Allowed : 10.76 % Favored : 87.05 % 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: 1.28 (0.20), residues: 1900 helix: 0.81 (0.19), residues: 840 sheet: 0.31 (0.34), residues: 235 loop : 1.36 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 340 HIS 0.003 0.001 HIS F 40 PHE 0.017 0.002 PHE H 375 TYR 0.011 0.001 TYR F 133 ARG 0.006 0.000 ARG F 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 195 time to evaluate : 1.757 Fit side-chains revert: symmetry clash REVERT: B 8 LEU cc_start: 0.9137 (OUTLIER) cc_final: 0.8937 (tt) REVERT: D 132 MET cc_start: 0.8006 (tmm) cc_final: 0.7529 (tmm) REVERT: D 270 GLU cc_start: 0.8038 (pm20) cc_final: 0.7441 (pt0) REVERT: E 8 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7872 (mtmt) REVERT: F 289 ILE cc_start: 0.8757 (mm) cc_final: 0.8473 (mm) REVERT: G 9 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7335 (ttmm) REVERT: I 12 ASN cc_start: 0.7287 (m-40) cc_final: 0.6976 (p0) REVERT: I 95 ARG cc_start: 0.7993 (mmm160) cc_final: 0.7725 (mmt-90) REVERT: I 141 SER cc_start: 0.8925 (m) cc_final: 0.8694 (m) REVERT: I 154 ASP cc_start: 0.8307 (t0) cc_final: 0.7940 (t70) REVERT: I 289 ILE cc_start: 0.8496 (mm) cc_final: 0.8177 (mm) outliers start: 36 outliers final: 18 residues processed: 218 average time/residue: 0.2479 time to fit residues: 82.9594 Evaluate side-chains 195 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 174 time to evaluate : 1.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 357 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 152 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 136 optimal weight: 6.9990 chunk 75 optimal weight: 0.7980 chunk 156 optimal weight: 10.0000 chunk 126 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN B 101 HIS D 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 15880 Z= 0.366 Angle : 0.655 7.480 21530 Z= 0.322 Chirality : 0.049 0.184 2400 Planarity : 0.004 0.062 2720 Dihedral : 8.067 89.641 2245 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.86 % Allowed : 11.91 % Favored : 85.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.19), residues: 1900 helix: 0.53 (0.18), residues: 840 sheet: -0.19 (0.28), residues: 310 loop : 1.27 (0.23), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.006 0.001 HIS F 88 PHE 0.031 0.002 PHE H 352 TYR 0.015 0.002 TYR I 143 ARG 0.007 0.001 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 181 time to evaluate : 1.774 Fit side-chains REVERT: A 1 MET cc_start: 0.5972 (ptt) cc_final: 0.4809 (mpp) REVERT: B 289 ILE cc_start: 0.8898 (mm) cc_final: 0.8626 (mt) REVERT: D 132 MET cc_start: 0.8036 (tmm) cc_final: 0.7621 (tmm) REVERT: D 248 ILE cc_start: 0.8924 (OUTLIER) cc_final: 0.8643 (pt) REVERT: E 6 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8224 (mt) REVERT: E 8 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7874 (mtmt) REVERT: F 176 MET cc_start: 0.7993 (mmm) cc_final: 0.7704 (mmt) REVERT: F 234 SER cc_start: 0.7688 (p) cc_final: 0.7170 (m) REVERT: F 289 ILE cc_start: 0.8899 (mm) cc_final: 0.8674 (mm) REVERT: G 9 LYS cc_start: 0.7781 (OUTLIER) cc_final: 0.7475 (ttpp) REVERT: I 95 ARG cc_start: 0.8064 (mmm160) cc_final: 0.7566 (mmt180) REVERT: I 289 ILE cc_start: 0.8622 (mm) cc_final: 0.8342 (mm) REVERT: I 300 SER cc_start: 0.8389 (p) cc_final: 0.8050 (m) outliers start: 47 outliers final: 31 residues processed: 212 average time/residue: 0.2422 time to fit residues: 79.6967 Evaluate side-chains 198 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 163 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 VAL Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 82 MET Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 7 ILE Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain G residue 12 SER Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 96 VAL Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 250 ILE Chi-restraints excluded: chain I residue 357 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 61 optimal weight: 1.9990 chunk 165 optimal weight: 0.0570 chunk 36 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 183 optimal weight: 0.9990 chunk 152 optimal weight: 10.0000 chunk 85 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 60 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 overall best weight: 0.9704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 115 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15880 Z= 0.189 Angle : 0.561 7.258 21530 Z= 0.271 Chirality : 0.046 0.183 2400 Planarity : 0.004 0.057 2720 Dihedral : 7.602 87.678 2245 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.82 % Allowed : 12.89 % Favored : 85.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.20), residues: 1900 helix: 0.78 (0.19), residues: 840 sheet: -0.07 (0.33), residues: 235 loop : 1.20 (0.22), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 340 HIS 0.004 0.001 HIS F 371 PHE 0.023 0.001 PHE H 352 TYR 0.010 0.001 TYR D 294 ARG 0.004 0.000 ARG D 372 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 182 time to evaluate : 1.764 Fit side-chains REVERT: A 1 MET cc_start: 0.5743 (ptt) cc_final: 0.4787 (mtm) REVERT: D 132 MET cc_start: 0.7903 (tmm) cc_final: 0.7557 (tmm) REVERT: D 248 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8484 (pt) REVERT: D 283 MET cc_start: 0.8626 (mmm) cc_final: 0.8346 (mmp) REVERT: E 6 LEU cc_start: 0.8436 (OUTLIER) cc_final: 0.8183 (mt) REVERT: E 8 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7828 (mtmt) REVERT: F 289 ILE cc_start: 0.8782 (mm) cc_final: 0.8554 (mm) REVERT: G 9 LYS cc_start: 0.7784 (OUTLIER) cc_final: 0.7432 (ttmm) REVERT: I 56 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8285 (t0) REVERT: I 95 ARG cc_start: 0.7994 (mmm160) cc_final: 0.7556 (mmt180) REVERT: I 137 GLN cc_start: 0.8413 (mp10) cc_final: 0.8208 (mt0) REVERT: I 289 ILE cc_start: 0.8447 (mm) cc_final: 0.8224 (mm) outliers start: 30 outliers final: 17 residues processed: 199 average time/residue: 0.2373 time to fit residues: 73.4745 Evaluate side-chains 184 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 357 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 177 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 134 optimal weight: 4.9990 chunk 154 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 chunk 114 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.5226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 15880 Z= 0.272 Angle : 0.593 6.455 21530 Z= 0.289 Chirality : 0.047 0.169 2400 Planarity : 0.004 0.058 2720 Dihedral : 7.698 80.315 2245 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.07 % Allowed : 13.62 % Favored : 84.32 % 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: 0.93 (0.19), residues: 1900 helix: 0.68 (0.19), residues: 845 sheet: -0.03 (0.31), residues: 265 loop : 1.07 (0.22), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 340 HIS 0.005 0.001 HIS F 88 PHE 0.016 0.002 PHE H 375 TYR 0.014 0.001 TYR D 294 ARG 0.004 0.000 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 167 time to evaluate : 1.714 Fit side-chains REVERT: A 1 MET cc_start: 0.5696 (ptt) cc_final: 0.4915 (mtm) REVERT: D 132 MET cc_start: 0.8025 (tmm) cc_final: 0.7610 (tmm) REVERT: D 248 ILE cc_start: 0.8881 (OUTLIER) cc_final: 0.8557 (pt) REVERT: D 283 MET cc_start: 0.8654 (mmm) cc_final: 0.8390 (mmp) REVERT: H 352 PHE cc_start: 0.8752 (t80) cc_final: 0.8418 (t80) REVERT: E 6 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8205 (mt) REVERT: E 8 LYS cc_start: 0.8344 (OUTLIER) cc_final: 0.7802 (mtmt) REVERT: F 289 ILE cc_start: 0.8885 (mm) cc_final: 0.8648 (mm) REVERT: G 9 LYS cc_start: 0.7833 (OUTLIER) cc_final: 0.7461 (ttmm) REVERT: I 95 ARG cc_start: 0.8052 (mmm160) cc_final: 0.7613 (mmt180) REVERT: I 289 ILE cc_start: 0.8476 (mm) cc_final: 0.8261 (mm) outliers start: 34 outliers final: 25 residues processed: 187 average time/residue: 0.2675 time to fit residues: 78.5081 Evaluate side-chains 188 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 159 time to evaluate : 1.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain E residue 6 LEU Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 7 ILE Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 357 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 73 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 55 optimal weight: 0.5980 chunk 35 optimal weight: 6.9990 chunk 116 optimal weight: 7.9990 chunk 124 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 175 optimal weight: 0.8980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15880 Z= 0.178 Angle : 0.563 8.251 21530 Z= 0.270 Chirality : 0.045 0.160 2400 Planarity : 0.004 0.053 2720 Dihedral : 7.424 77.199 2245 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.13 % Allowed : 13.56 % Favored : 84.32 % 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: 1.12 (0.20), residues: 1900 helix: 0.83 (0.19), residues: 845 sheet: 0.03 (0.34), residues: 225 loop : 1.14 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 340 HIS 0.003 0.001 HIS F 371 PHE 0.014 0.001 PHE H 375 TYR 0.010 0.001 TYR D 133 ARG 0.004 0.000 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 174 time to evaluate : 1.656 Fit side-chains REVERT: A 1 MET cc_start: 0.5389 (ptt) cc_final: 0.5090 (ptm) REVERT: D 132 MET cc_start: 0.7875 (tmm) cc_final: 0.7546 (tmm) REVERT: D 248 ILE cc_start: 0.8850 (OUTLIER) cc_final: 0.8444 (pt) REVERT: D 283 MET cc_start: 0.8668 (mmm) cc_final: 0.8416 (mmp) REVERT: E 8 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.7785 (mtmt) REVERT: F 289 ILE cc_start: 0.8794 (mm) cc_final: 0.8502 (mm) REVERT: G 9 LYS cc_start: 0.7912 (OUTLIER) cc_final: 0.7538 (ttmm) REVERT: I 56 ASP cc_start: 0.8699 (OUTLIER) cc_final: 0.8443 (t0) REVERT: I 95 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7610 (mmt180) REVERT: I 289 ILE cc_start: 0.8389 (mm) cc_final: 0.8090 (mm) outliers start: 35 outliers final: 25 residues processed: 195 average time/residue: 0.2413 time to fit residues: 72.8268 Evaluate side-chains 196 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain A residue 13 ILE Chi-restraints excluded: chain B residue 119 MET Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 278 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 194 THR Chi-restraints excluded: chain I residue 357 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 160 optimal weight: 0.6980 chunk 170 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 74 optimal weight: 0.6980 chunk 134 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 154 optimal weight: 7.9990 chunk 161 optimal weight: 0.6980 chunk 112 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.5419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15880 Z= 0.166 Angle : 0.554 8.193 21530 Z= 0.266 Chirality : 0.045 0.159 2400 Planarity : 0.004 0.054 2720 Dihedral : 7.302 75.084 2245 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.95 % Allowed : 13.80 % Favored : 84.26 % 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: 1.20 (0.20), residues: 1900 helix: 0.93 (0.19), residues: 845 sheet: 0.05 (0.34), residues: 225 loop : 1.15 (0.22), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP D 340 HIS 0.003 0.001 HIS F 371 PHE 0.016 0.001 PHE H 375 TYR 0.023 0.001 TYR D 133 ARG 0.004 0.000 ARG F 372 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 179 time to evaluate : 1.748 Fit side-chains REVERT: A 1 MET cc_start: 0.5348 (ptt) cc_final: 0.4770 (mtm) REVERT: D 248 ILE cc_start: 0.8824 (OUTLIER) cc_final: 0.8398 (pt) REVERT: D 270 GLU cc_start: 0.7956 (pm20) cc_final: 0.7584 (pm20) REVERT: D 283 MET cc_start: 0.8666 (mmm) cc_final: 0.8417 (mmp) REVERT: E 8 LYS cc_start: 0.8327 (OUTLIER) cc_final: 0.7683 (mtmt) REVERT: F 289 ILE cc_start: 0.8798 (mm) cc_final: 0.8497 (mm) REVERT: F 355 MET cc_start: 0.7975 (mmm) cc_final: 0.7721 (tpp) REVERT: G 1 MET cc_start: 0.5479 (ptm) cc_final: 0.5104 (ptm) REVERT: G 9 LYS cc_start: 0.7849 (OUTLIER) cc_final: 0.7606 (ttmm) REVERT: I 56 ASP cc_start: 0.8686 (OUTLIER) cc_final: 0.8420 (t0) REVERT: I 95 ARG cc_start: 0.7945 (mmm160) cc_final: 0.7592 (mmt180) REVERT: I 289 ILE cc_start: 0.8362 (mm) cc_final: 0.8100 (mm) outliers start: 32 outliers final: 21 residues processed: 198 average time/residue: 0.2419 time to fit residues: 74.4667 Evaluate side-chains 192 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 167 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 6 THR Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 357 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 110 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 174 optimal weight: 0.9980 chunk 150 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 119 optimal weight: 4.9990 chunk 160 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN ** H 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 354 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.5483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15880 Z= 0.202 Angle : 0.568 8.331 21530 Z= 0.273 Chirality : 0.046 0.160 2400 Planarity : 0.004 0.054 2720 Dihedral : 7.276 74.016 2245 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.58 % Allowed : 14.29 % Favored : 84.13 % 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: 1.09 (0.20), residues: 1900 helix: 0.87 (0.19), residues: 845 sheet: -0.07 (0.32), residues: 265 loop : 1.13 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 340 HIS 0.003 0.001 HIS F 88 PHE 0.023 0.001 PHE D 352 TYR 0.032 0.001 TYR D 133 ARG 0.005 0.000 ARG D 372 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3800 Ramachandran restraints generated. 1900 Oldfield, 0 Emsley, 1900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.875 Fit side-chains REVERT: A 1 MET cc_start: 0.5374 (ptt) cc_final: 0.4835 (mtm) REVERT: B 47 MET cc_start: 0.6772 (ppp) cc_final: 0.6565 (ppp) REVERT: B 289 ILE cc_start: 0.8660 (mm) cc_final: 0.8404 (mt) REVERT: D 248 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8432 (pt) REVERT: D 270 GLU cc_start: 0.7923 (pm20) cc_final: 0.7485 (pm20) REVERT: D 283 MET cc_start: 0.8638 (mmm) cc_final: 0.8405 (mmp) REVERT: E 8 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7683 (mtmt) REVERT: F 289 ILE cc_start: 0.8839 (mm) cc_final: 0.8596 (mm) REVERT: F 355 MET cc_start: 0.7983 (mmm) cc_final: 0.7734 (tpp) REVERT: G 9 LYS cc_start: 0.7835 (OUTLIER) cc_final: 0.7573 (ttmm) REVERT: I 56 ASP cc_start: 0.8790 (OUTLIER) cc_final: 0.8521 (t0) REVERT: I 95 ARG cc_start: 0.7952 (mmm160) cc_final: 0.7590 (mmt180) REVERT: I 217 CYS cc_start: 0.8339 (m) cc_final: 0.7961 (m) REVERT: I 289 ILE cc_start: 0.8440 (mm) cc_final: 0.8106 (mm) outliers start: 26 outliers final: 20 residues processed: 183 average time/residue: 0.2732 time to fit residues: 76.5297 Evaluate side-chains 189 residues out of total 1645 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 165 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 LYS Chi-restraints excluded: chain B residue 151 ILE Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 234 SER Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain D residue 115 ASN Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 248 ILE Chi-restraints excluded: chain H residue 106 THR Chi-restraints excluded: chain H residue 132 MET Chi-restraints excluded: chain E residue 8 LYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 129 VAL Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 201 VAL Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 303 THR Chi-restraints excluded: chain F residue 325 MET Chi-restraints excluded: chain G residue 9 LYS Chi-restraints excluded: chain I residue 30 VAL Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 250 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 46 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 155 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.092504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.081957 restraints weight = 31200.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.084354 restraints weight = 15382.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.085997 restraints weight = 9238.134| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.5529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15880 Z= 0.191 Angle : 0.569 8.467 21530 Z= 0.273 Chirality : 0.045 0.159 2400 Planarity : 0.004 0.054 2720 Dihedral : 7.216 73.656 2245 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.58 % Allowed : 14.53 % Favored : 83.89 % 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: 1.09 (0.20), residues: 1900 helix: 0.89 (0.19), residues: 845 sheet: -0.11 (0.32), residues: 265 loop : 1.14 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 340 HIS 0.003 0.001 HIS F 371 PHE 0.023 0.001 PHE D 352 TYR 0.029 0.001 TYR D 133 ARG 0.007 0.000 ARG D 372 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2743.56 seconds wall clock time: 50 minutes 21.47 seconds (3021.47 seconds total)