Starting phenix.real_space_refine on Sun Mar 17 20:19:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/03_2024/7vy3_32193_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/03_2024/7vy3_32193.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/03_2024/7vy3_32193.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/03_2024/7vy3_32193.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/03_2024/7vy3_32193_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vy3_32193/03_2024/7vy3_32193_updated.pdb" } resolution = 2.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 16 5.49 5 Mg 25 5.21 5 S 69 5.16 5 C 13266 2.51 5 N 2513 2.21 5 O 2941 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 11": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18831 Number of models: 1 Model: "" Number of chains: 49 Chain: "L" Number of atoms: 2233 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2233 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 266} Chain: "M" Number of atoms: 2437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2437 Classifications: {'peptide': 306} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 293} Chain: "H" Number of atoms: 1867 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 246, 1864 Classifications: {'peptide': 246} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 222} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 1910 Chain: "A" Number of atoms: 386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 386 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 359 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "D" Number of atoms: 455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 455 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 365 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 453 Classifications: {'peptide': 54} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 457 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 347 Classifications: {'peptide': 43} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 41} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "S" Number of atoms: 454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 454 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 2, 'TRANS': 51} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "T" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "V" Number of atoms: 441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 441 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "W" Number of atoms: 339 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 339 Classifications: {'peptide': 42} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 40} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "Y" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 318 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain: "Z" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 261 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 1, 'TRANS': 29} Chain: "1" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 216 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 1, 'TRANS': 25} Chain: "X" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 401 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 4, 'TRANS': 47} Chain: "L" Number of atoms: 384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 384 Unusual residues: {'BCL': 2, 'BPH': 1, 'LDA': 1, 'LMT': 2, 'PGV': 1, 'U10': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'PGV:plan-3': 1, 'U10:plan-8': 2, 'U10:plan-9': 2, 'U10:plan-5': 1, 'U10:plan-6': 2, 'U10:plan-7': 2, 'U10:plan-10': 2, 'U10:plan-11': 2} Unresolved non-hydrogen planarities: 52 Chain: "M" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 472 Unusual residues: {' FE': 1, 'BCL': 2, 'BPH': 1, 'CDL': 1, 'LMT': 2, 'PGV': 1, 'SPO': 1, 'U10': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 65 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 270 Unusual residues: {'CDL': 1, 'LDA': 1, 'LMT': 3, 'PGV': 1, 'PTY': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 52 Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 177 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "D" Number of atoms: 240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 240 Unusual residues: {'BCL': 1, 'LMT': 1, 'SPO': 2, 'U10': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 260 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 2, 'PTY': 1, 'SPO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 5 Chain: "G" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 119 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 119 Unusual residues: {'BCL': 1, 'LMT': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 18 Chain: "J" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 226 Unusual residues: {'BCL': 1, 'LMT': 1, 'PGV': 1, 'SPO': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Chain: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 256 Unusual residues: {'BCL': 2, 'LMT': 2, 'PGV': 1, 'SPO': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 3 Chain: "S" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "T" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 156 Unusual residues: {'BCL': 1, 'CDL': 1, 'LDA': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 9 Chain: "Z" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 13 Unusual residues: {'LDA': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 11.40, per 1000 atoms: 0.61 Number of scatterers: 18831 At special positions: 0 Unit cell: (121.36, 125.46, 113.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 69 16.00 P 16 15.00 Mg 25 11.99 O 2941 8.00 N 2513 7.00 C 13266 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 - 3.50 Amino acid : False - 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=24, symmetry=0 Number of additional bonds: simple=24, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.50 Conformation dependent library (CDL) restraints added in 2.9 seconds 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 77 helices and 5 sheets defined 63.5% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 Creating SS restraints... Processing helix chain 'L' and resid 7 through 9 No H-bonds generated for 'chain 'L' and resid 7 through 9' Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 71 through 73 No H-bonds generated for 'chain 'L' and resid 71 through 73' Processing helix chain 'L' and resid 84 through 111 Processing helix chain 'L' and resid 116 through 132 removed outlier: 3.553A pdb=" N PHE L 123 " --> pdb=" O PHE L 119 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA L 124 " --> pdb=" O ALA L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 139 Processing helix chain 'L' and resid 142 through 144 No H-bonds generated for 'chain 'L' and resid 142 through 144' Processing helix chain 'L' and resid 152 through 164 removed outlier: 4.171A pdb=" N TYR L 164 " --> pdb=" O THR L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 169 No H-bonds generated for 'chain 'L' and resid 167 through 169' Processing helix chain 'L' and resid 171 through 198 Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 226 through 249 removed outlier: 3.866A pdb=" N HIS L 230 " --> pdb=" O THR L 226 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 267 removed outlier: 3.509A pdb=" N VAL L 267 " --> pdb=" O GLN L 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 54 through 77 Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 99 through 101 No H-bonds generated for 'chain 'M' and resid 99 through 101' Processing helix chain 'M' and resid 109 through 111 No H-bonds generated for 'chain 'M' and resid 109 through 111' Processing helix chain 'M' and resid 113 through 139 Processing helix chain 'M' and resid 145 through 161 removed outlier: 3.628A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 168 Processing helix chain 'M' and resid 171 through 173 No H-bonds generated for 'chain 'M' and resid 171 through 173' Processing helix chain 'M' and resid 179 through 192 removed outlier: 3.801A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 198 No H-bonds generated for 'chain 'M' and resid 196 through 198' Processing helix chain 'M' and resid 200 through 229 removed outlier: 4.862A pdb=" N ARG M 228 " --> pdb=" O LEU M 224 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N PHE M 229 " --> pdb=" O ALA M 225 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 239 Processing helix chain 'M' and resid 243 through 256 removed outlier: 3.664A pdb=" N TRP M 252 " --> pdb=" O ALA M 248 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 286 removed outlier: 3.983A pdb=" N VAL M 276 " --> pdb=" O MET M 272 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N THR M 277 " --> pdb=" O ALA M 273 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 301 Processing helix chain 'H' and resid 12 through 34 Processing helix chain 'H' and resid 104 through 107 No H-bonds generated for 'chain 'H' and resid 104 through 107' Processing helix chain 'H' and resid 110 through 112 No H-bonds generated for 'chain 'H' and resid 110 through 112' Processing helix chain 'H' and resid 193 through 195 No H-bonds generated for 'chain 'H' and resid 193 through 195' Processing helix chain 'H' and resid 210 through 215 removed outlier: 3.705A pdb=" N PHE H 213 " --> pdb=" O SER H 210 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N ALA H 214 " --> pdb=" O ASP H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 243 removed outlier: 3.508A pdb=" N GLY H 240 " --> pdb=" O TYR H 236 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU H 241 " --> pdb=" O VAL H 237 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET H 242 " --> pdb=" O ALA H 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 4 through 9 Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.569A pdb=" N VAL A 18 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 44 Processing helix chain 'D' and resid 4 through 9 Processing helix chain 'D' and resid 13 through 37 Processing helix chain 'D' and resid 43 through 50 Processing helix chain 'E' and resid 13 through 44 Processing helix chain 'F' and resid 4 through 9 Processing helix chain 'F' and resid 13 through 37 Processing helix chain 'F' and resid 43 through 50 Processing helix chain 'G' and resid 13 through 44 Processing helix chain 'I' and resid 4 through 7 Processing helix chain 'I' and resid 13 through 37 Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 43 through 51 removed outlier: 3.505A pdb=" N ALA I 48 " --> pdb=" O LEU I 44 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 44 Processing helix chain 'K' and resid 4 through 9 Processing helix chain 'K' and resid 13 through 37 Processing helix chain 'K' and resid 43 through 50 Processing helix chain 'N' and resid 13 through 44 Processing helix chain 'O' and resid 4 through 10 Processing helix chain 'O' and resid 13 through 37 removed outlier: 3.552A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 43 through 51 Processing helix chain 'P' and resid 15 through 44 Processing helix chain 'Q' and resid 4 through 9 Processing helix chain 'Q' and resid 13 through 37 Processing helix chain 'Q' and resid 43 through 51 Processing helix chain 'R' and resid 13 through 44 Processing helix chain 'S' and resid 4 through 7 Processing helix chain 'S' and resid 13 through 37 Processing helix chain 'S' and resid 43 through 50 Processing helix chain 'T' and resid 13 through 44 Processing helix chain 'V' and resid 4 through 10 removed outlier: 3.830A pdb=" N ILE V 10 " --> pdb=" O ILE V 7 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 37 Processing helix chain 'V' and resid 43 through 51 Processing helix chain 'W' and resid 13 through 44 removed outlier: 4.144A pdb=" N GLU W 18 " --> pdb=" O GLU W 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 13 through 37 removed outlier: 3.943A pdb=" N PHE Y 17 " --> pdb=" O PRO Y 13 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL Y 18 " --> pdb=" O ARG Y 14 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 41 No H-bonds generated for 'chain 'Y' and resid 39 through 41' Processing helix chain 'Y' and resid 43 through 46 No H-bonds generated for 'chain 'Y' and resid 43 through 46' Processing helix chain 'Z' and resid 19 through 44 removed outlier: 3.629A pdb=" N SER Z 25 " --> pdb=" O SER Z 21 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY Z 26 " --> pdb=" O VAL Z 22 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL Z 33 " --> pdb=" O LEU Z 29 " (cutoff:3.500A) Processing helix chain '1' and resid 13 through 37 Processing helix chain 'X' and resid 18 through 54 Processing sheet with id= A, first strand: chain 'L' and resid 24 through 26 removed outlier: 3.573A pdb=" N PHE L 24 " --> pdb=" O VAL L 31 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'H' and resid 62 through 65 Processing sheet with id= C, first strand: chain 'H' and resid 87 through 89 Processing sheet with id= D, first strand: chain 'H' and resid 131 through 133 removed outlier: 6.695A pdb=" N GLU H 180 " --> pdb=" O VAL H 165 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ILE H 167 " --> pdb=" O PHE H 178 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N PHE H 178 " --> pdb=" O ILE H 167 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'H' and resid 202 through 204 removed outlier: 3.656A pdb=" N GLY H 162 " --> pdb=" O VAL H 153 " (cutoff:3.500A) 880 hydrogen bonds defined for protein. 2547 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.79 Time building geometry restraints manager: 9.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 5433 1.37 - 1.54: 13750 1.54 - 1.71: 111 1.71 - 1.88: 133 1.88 - 2.05: 100 Bond restraints: 19527 Sorted by residual: bond pdb=" CA7 CDL M 408 " pdb=" OA8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.458 -0.124 1.10e-02 8.26e+03 1.27e+02 bond pdb=" CA7 CDL H 307 " pdb=" OA8 CDL H 307 " ideal model delta sigma weight residual 1.334 1.455 -0.121 1.10e-02 8.26e+03 1.21e+02 bond pdb=" CA7 CDL Y 102 " pdb=" OA8 CDL Y 102 " ideal model delta sigma weight residual 1.334 1.454 -0.120 1.10e-02 8.26e+03 1.20e+02 bond pdb=" CB7 CDL H 307 " pdb=" OB8 CDL H 307 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.16e+02 bond pdb=" CB7 CDL M 408 " pdb=" OB8 CDL M 408 " ideal model delta sigma weight residual 1.334 1.452 -0.118 1.10e-02 8.26e+03 1.15e+02 ... (remaining 19522 not shown) Histogram of bond angle deviations from ideal: 83.96 - 102.73: 367 102.73 - 121.50: 21883 121.50 - 140.27: 4369 140.27 - 159.04: 28 159.04 - 177.81: 49 Bond angle restraints: 26696 Sorted by residual: angle pdb=" C2 SPO P 102 " pdb=" C1 SPO P 102 " pdb=" C4 SPO P 102 " ideal model delta sigma weight residual 110.23 85.50 24.73 3.00e+00 1.11e-01 6.80e+01 angle pdb=" C1D BCL 1 101 " pdb=" C2D BCL 1 101 " pdb=" CMD BCL 1 101 " ideal model delta sigma weight residual 125.57 139.20 -13.63 1.83e+00 2.99e-01 5.56e+01 angle pdb=" C1D BCL M 402 " pdb=" C2D BCL M 402 " pdb=" CMD BCL M 402 " ideal model delta sigma weight residual 125.57 139.15 -13.57 1.83e+00 2.99e-01 5.51e+01 angle pdb=" C1D BCL Y 103 " pdb=" C2D BCL Y 103 " pdb=" CMD BCL Y 103 " ideal model delta sigma weight residual 125.57 139.15 -13.57 1.83e+00 2.99e-01 5.51e+01 angle pdb=" C1D BCL L 301 " pdb=" C2D BCL L 301 " pdb=" CMD BCL L 301 " ideal model delta sigma weight residual 125.57 139.13 -13.55 1.83e+00 2.99e-01 5.50e+01 ... (remaining 26691 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.92: 10498 35.92 - 71.85: 496 71.85 - 107.77: 130 107.77 - 143.69: 46 143.69 - 179.61: 12 Dihedral angle restraints: 11182 sinusoidal: 5859 harmonic: 5323 Sorted by residual: dihedral pdb=" C1 BCL L 309 " pdb=" C2 BCL L 309 " pdb=" C3 BCL L 309 " pdb=" C5 BCL L 309 " ideal model delta sinusoidal sigma weight residual -180.00 -0.95 -179.05 1 8.00e+00 1.56e-02 3.00e+02 dihedral pdb=" C1 BCL B 103 " pdb=" CGA BCL B 103 " pdb=" O2A BCL B 103 " pdb=" CBA BCL B 103 " ideal model delta sinusoidal sigma weight residual 180.00 116.19 63.81 1 6.00e+00 2.78e-02 1.49e+02 dihedral pdb=" CBD BCL Z 102 " pdb=" CGD BCL Z 102 " pdb=" O2D BCL Z 102 " pdb=" CED BCL Z 102 " ideal model delta sinusoidal sigma weight residual 180.00 140.82 39.18 1 5.00e+00 4.00e-02 8.63e+01 ... (remaining 11179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 2177 0.059 - 0.118: 360 0.118 - 0.177: 102 0.177 - 0.236: 18 0.236 - 0.295: 10 Chirality restraints: 2667 Sorted by residual: chirality pdb=" C05 PGV H 301 " pdb=" C04 PGV H 301 " pdb=" C06 PGV H 301 " pdb=" O05 PGV H 301 " both_signs ideal model delta sigma weight residual False 2.29 2.59 -0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" C05 PGV M 409 " pdb=" C04 PGV M 409 " pdb=" C06 PGV M 409 " pdb=" O05 PGV M 409 " both_signs ideal model delta sigma weight residual False 2.29 2.58 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" C05 PGV F 102 " pdb=" C04 PGV F 102 " pdb=" C06 PGV F 102 " pdb=" O05 PGV F 102 " both_signs ideal model delta sigma weight residual False 2.29 2.57 -0.28 2.00e-01 2.50e+01 1.90e+00 ... (remaining 2664 not shown) Planarity restraints: 3163 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 U10 D 105 " 0.062 2.00e-02 2.50e+03 1.93e-01 6.53e+02 pdb=" C1M U10 D 105 " -0.255 2.00e-02 2.50e+03 pdb=" C2 U10 D 105 " 0.145 2.00e-02 2.50e+03 pdb=" C3 U10 D 105 " 0.096 2.00e-02 2.50e+03 pdb=" C4 U10 D 105 " -0.289 2.00e-02 2.50e+03 pdb=" C5 U10 D 105 " -0.037 2.00e-02 2.50e+03 pdb=" C6 U10 D 105 " 0.278 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL B 103 " 0.343 3.00e-02 1.11e+03 2.80e-01 4.36e+02 pdb=" CBA BCL B 103 " 0.182 3.00e-02 1.11e+03 pdb=" CGA BCL B 103 " -0.077 3.00e-02 1.11e+03 pdb=" O1A BCL B 103 " 0.037 3.00e-02 1.11e+03 pdb=" O2A BCL B 103 " -0.485 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1C BCL 1 101 " -0.310 3.10e-02 1.04e+03 2.87e-01 4.30e+02 pdb=" C4C BCL 1 101 " -0.265 3.10e-02 1.04e+03 pdb=" CHC BCL 1 101 " 0.055 3.10e-02 1.04e+03 pdb=" CHD BCL 1 101 " 0.028 3.10e-02 1.04e+03 pdb=" NC BCL 1 101 " 0.492 3.10e-02 1.04e+03 ... (remaining 3160 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 176 2.61 - 3.18: 14761 3.18 - 3.75: 31504 3.75 - 4.33: 46656 4.33 - 4.90: 73889 Nonbonded interactions: 166986 Sorted by model distance: nonbonded pdb=" OE2 GLU M 234 " pdb="FE FE M 404 " model vdw 2.032 2.260 nonbonded pdb=" OE1 GLU M 234 " pdb="FE FE M 404 " model vdw 2.066 2.260 nonbonded pdb=" OG SER A 37 " pdb=" O2' LMT A 102 " model vdw 2.102 2.440 nonbonded pdb=" NE2 HIS L 190 " pdb="FE FE M 404 " model vdw 2.119 2.340 nonbonded pdb=" OE1 GLN S 20 " pdb=" OH TYR T 23 " model vdw 2.184 2.440 ... (remaining 166981 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 45)) selection = (chain 'O' and resid 3 through 45) selection = (chain 'V' and ((resid 3 and (name N or name CA or name C or name O or name CB ) \ ) or resid 4 through 45)) } ncs_group { reference = (chain 'B' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'E' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'G' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'J' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'N' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'P' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'R' and resid 7 through 48) selection = (chain 'T' and (resid 7 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 48)) selection = (chain 'W' and resid 7 through 48) } ncs_group { reference = (chain 'D' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 54)) selection = (chain 'F' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'I' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'K' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'Q' and ((resid 1 and (name N or name CA or name C or name O or name CB o \ r name CN or name O1 )) or resid 2 through 53 or (resid 54 and (name N or name C \ A or name C or name O or name CB )))) selection = (chain 'S' and (resid 1 through 53 or (resid 54 and (name N or name CA or name C \ or name O or name CB )))) } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 10.900 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 51.850 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 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 : 0.019 0.183 19527 Z= 0.959 Angle : 1.837 24.733 26696 Z= 0.773 Chirality : 0.053 0.295 2667 Planarity : 0.017 0.287 3163 Dihedral : 23.059 179.613 7766 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.30 % Allowed : 3.49 % Favored : 94.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1789 helix: 1.12 (0.14), residues: 1147 sheet: -0.62 (1.08), residues: 24 loop : 0.25 (0.26), residues: 618 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP M 268 HIS 0.005 0.001 HIS L 153 PHE 0.015 0.001 PHE H 10 TYR 0.011 0.001 TYR L 164 ARG 0.003 0.001 ARG G 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 289 time to evaluate : 1.882 Fit side-chains REVERT: M 168 MET cc_start: 0.8939 (mmm) cc_final: 0.8511 (mmm) REVERT: H 134 MET cc_start: 0.8539 (ttp) cc_final: 0.8230 (ttp) REVERT: A 37 SER cc_start: 0.8204 (t) cc_final: 0.7987 (t) REVERT: G 42 TYR cc_start: 0.8853 (t80) cc_final: 0.8559 (t80) REVERT: I 3 LYS cc_start: 0.8496 (mttt) cc_final: 0.8290 (mttm) REVERT: O 24 LEU cc_start: 0.8911 (OUTLIER) cc_final: 0.8478 (mp) REVERT: S 52 ASN cc_start: 0.7630 (m110) cc_final: 0.7111 (m110) REVERT: Z 24 MET cc_start: 0.5136 (mmm) cc_final: 0.4558 (mtp) REVERT: 1 36 LEU cc_start: 0.4018 (OUTLIER) cc_final: 0.3314 (mt) REVERT: X 29 LYS cc_start: 0.7647 (ttpt) cc_final: 0.7406 (ttmm) REVERT: X 47 PHE cc_start: 0.7735 (t80) cc_final: 0.7494 (t80) outliers start: 35 outliers final: 15 residues processed: 317 average time/residue: 1.1665 time to fit residues: 419.2783 Evaluate side-chains 230 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 213 time to evaluate : 1.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 102 LEU Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain O residue 24 LEU Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain V residue 9 MET Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain 1 residue 36 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 89 optimal weight: 1.9990 chunk 70 optimal weight: 10.0000 chunk 137 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 chunk 158 optimal weight: 30.0000 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 301 HIS H 199 GLN A 20 GLN B 15 GLN E 17 GLN F 20 GLN I 20 GLN N 17 GLN V 20 GLN Y 20 GLN 1 20 GLN X 66 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19527 Z= 0.180 Angle : 0.727 14.546 26696 Z= 0.277 Chirality : 0.040 0.466 2667 Planarity : 0.004 0.038 3163 Dihedral : 21.020 179.533 4608 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 3.62 % Allowed : 8.82 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.09 (0.19), residues: 1789 helix: 2.02 (0.14), residues: 1162 sheet: -0.58 (1.12), residues: 24 loop : 0.32 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 252 HIS 0.009 0.001 HIS L 153 PHE 0.014 0.001 PHE H 20 TYR 0.012 0.001 TYR K 5 ARG 0.007 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 220 time to evaluate : 1.825 Fit side-chains REVERT: L 72 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7608 (pt0) REVERT: M 100 GLU cc_start: 0.7388 (OUTLIER) cc_final: 0.7137 (pm20) REVERT: M 218 MET cc_start: 0.9069 (mtp) cc_final: 0.8599 (mtp) REVERT: H 134 MET cc_start: 0.8494 (ttp) cc_final: 0.8181 (ttp) REVERT: A 37 SER cc_start: 0.8249 (t) cc_final: 0.7981 (t) REVERT: G 42 TYR cc_start: 0.8877 (t80) cc_final: 0.8591 (t80) REVERT: S 20 GLN cc_start: 0.7752 (OUTLIER) cc_final: 0.7505 (tt0) REVERT: S 52 ASN cc_start: 0.7606 (m110) cc_final: 0.7059 (m110) REVERT: V 45 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7140 (mm-30) REVERT: W 31 SER cc_start: 0.8191 (m) cc_final: 0.7878 (m) REVERT: Z 24 MET cc_start: 0.5192 (mmm) cc_final: 0.4485 (mtp) REVERT: 1 36 LEU cc_start: 0.4072 (OUTLIER) cc_final: 0.3411 (mt) REVERT: X 67 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.7006 (pp) outliers start: 55 outliers final: 20 residues processed: 250 average time/residue: 1.2001 time to fit residues: 339.3395 Evaluate side-chains 230 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 204 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain V residue 45 GLU Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain 1 residue 36 LEU Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 108 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 171 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 157 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 264 GLN H 44 ASN E 15 GLN E 17 GLN N 17 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19527 Z= 0.321 Angle : 0.803 16.556 26696 Z= 0.316 Chirality : 0.044 0.478 2667 Planarity : 0.004 0.038 3163 Dihedral : 19.924 179.610 4597 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.62 % Allowed : 10.66 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.86 (0.19), residues: 1789 helix: 1.85 (0.14), residues: 1163 sheet: -0.83 (1.08), residues: 24 loop : 0.22 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP M 271 HIS 0.013 0.002 HIS L 153 PHE 0.027 0.002 PHE H 20 TYR 0.015 0.002 TYR L 164 ARG 0.006 0.001 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 202 time to evaluate : 1.775 Fit side-chains REVERT: M 100 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.7181 (pm20) REVERT: M 218 MET cc_start: 0.9045 (mtp) cc_final: 0.8637 (mtp) REVERT: H 134 MET cc_start: 0.8550 (ttp) cc_final: 0.8284 (ttp) REVERT: D 20 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8683 (tt0) REVERT: I 3 LYS cc_start: 0.8419 (mttm) cc_final: 0.8189 (mttt) REVERT: S 20 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7585 (tt0) REVERT: W 31 SER cc_start: 0.8300 (m) cc_final: 0.8029 (m) REVERT: W 43 ILE cc_start: 0.8138 (OUTLIER) cc_final: 0.7878 (mp) REVERT: Y 30 MET cc_start: 0.4689 (tmm) cc_final: 0.4472 (tmm) REVERT: Z 24 MET cc_start: 0.5213 (mmm) cc_final: 0.4514 (mtp) REVERT: X 67 ILE cc_start: 0.7387 (OUTLIER) cc_final: 0.7072 (pp) outliers start: 55 outliers final: 26 residues processed: 235 average time/residue: 1.3076 time to fit residues: 346.2459 Evaluate side-chains 227 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 196 time to evaluate : 1.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 6 LEU Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 20 GLN Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 157 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 75 optimal weight: 4.9990 chunk 106 optimal weight: 0.5980 chunk 159 optimal weight: 9.9990 chunk 169 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 151 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 19527 Z= 0.166 Angle : 0.651 14.398 26696 Z= 0.251 Chirality : 0.038 0.505 2667 Planarity : 0.003 0.038 3163 Dihedral : 18.378 179.658 4595 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.83 % Allowed : 11.39 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.33 (0.19), residues: 1789 helix: 2.29 (0.14), residues: 1164 sheet: -0.56 (1.12), residues: 24 loop : 0.23 (0.26), residues: 601 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 157 HIS 0.009 0.001 HIS L 153 PHE 0.018 0.001 PHE H 20 TYR 0.010 0.001 TYR K 5 ARG 0.005 0.000 ARG O 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 215 time to evaluate : 1.592 Fit side-chains REVERT: L 72 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: L 216 PHE cc_start: 0.8655 (m-80) cc_final: 0.8417 (m-80) REVERT: H 134 MET cc_start: 0.8530 (ttp) cc_final: 0.8183 (ttp) REVERT: G 42 TYR cc_start: 0.8899 (t80) cc_final: 0.8612 (t80) REVERT: N 24 MET cc_start: 0.8880 (mmm) cc_final: 0.8464 (mmm) REVERT: W 24 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7417 (mmm) REVERT: W 27 LEU cc_start: 0.7689 (tt) cc_final: 0.7271 (tm) REVERT: W 31 SER cc_start: 0.8240 (m) cc_final: 0.7911 (m) REVERT: W 43 ILE cc_start: 0.8090 (OUTLIER) cc_final: 0.7888 (mp) REVERT: Z 24 MET cc_start: 0.4970 (mmm) cc_final: 0.4386 (mtp) REVERT: X 67 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7075 (pp) outliers start: 43 outliers final: 20 residues processed: 240 average time/residue: 1.2110 time to fit residues: 328.6211 Evaluate side-chains 227 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 203 time to evaluate : 1.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 72 GLU Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 206 ASN Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 24 MET Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 140 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 125 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 144 optimal weight: 8.9990 chunk 116 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 42 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 206 ASN E 17 GLN K 20 GLN N 17 GLN ** V 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 26 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.080 19527 Z= 0.447 Angle : 0.889 16.736 26696 Z= 0.351 Chirality : 0.048 0.477 2667 Planarity : 0.005 0.052 3163 Dihedral : 19.585 179.289 4588 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.82 % Allowed : 10.53 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.56 (0.19), residues: 1789 helix: 1.65 (0.14), residues: 1155 sheet: -1.04 (1.04), residues: 24 loop : 0.05 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP M 271 HIS 0.014 0.002 HIS L 153 PHE 0.033 0.002 PHE H 20 TYR 0.019 0.003 TYR L 164 ARG 0.006 0.001 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 198 time to evaluate : 1.702 Fit side-chains REVERT: M 100 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: M 218 MET cc_start: 0.8941 (mtp) cc_final: 0.8621 (mtp) REVERT: H 134 MET cc_start: 0.8559 (ttp) cc_final: 0.8155 (ttp) REVERT: F 30 MET cc_start: 0.7481 (tpt) cc_final: 0.7230 (mmm) REVERT: T 19 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7511 (tp) REVERT: W 24 MET cc_start: 0.7708 (OUTLIER) cc_final: 0.7463 (mmm) REVERT: W 27 LEU cc_start: 0.7743 (tt) cc_final: 0.7541 (tm) REVERT: W 43 ILE cc_start: 0.8140 (OUTLIER) cc_final: 0.7880 (mp) REVERT: Z 24 MET cc_start: 0.5280 (mmm) cc_final: 0.4582 (mtp) REVERT: X 67 ILE cc_start: 0.7371 (OUTLIER) cc_final: 0.7069 (pp) outliers start: 58 outliers final: 30 residues processed: 233 average time/residue: 1.2328 time to fit residues: 324.7460 Evaluate side-chains 230 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 1.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 114 LEU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain H residue 231 ASP Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain G residue 14 GLU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 24 MET Chi-restraints excluded: chain W residue 35 ILE Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 56 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 chunk 33 optimal weight: 8.9990 chunk 99 optimal weight: 0.5980 chunk 41 optimal weight: 0.9980 chunk 169 optimal weight: 5.9990 chunk 140 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19527 Z= 0.248 Angle : 0.716 15.684 26696 Z= 0.281 Chirality : 0.041 0.479 2667 Planarity : 0.004 0.039 3163 Dihedral : 18.534 179.493 4586 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.55 % Allowed : 10.73 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.97 (0.19), residues: 1789 helix: 1.99 (0.14), residues: 1163 sheet: -0.80 (1.07), residues: 24 loop : 0.13 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP M 271 HIS 0.012 0.001 HIS L 153 PHE 0.025 0.002 PHE H 20 TYR 0.013 0.002 TYR I 41 ARG 0.005 0.001 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 200 time to evaluate : 1.735 Fit side-chains REVERT: M 100 GLU cc_start: 0.7391 (OUTLIER) cc_final: 0.7185 (pm20) REVERT: M 218 MET cc_start: 0.8942 (mtp) cc_final: 0.8551 (mtp) REVERT: H 134 MET cc_start: 0.8555 (ttp) cc_final: 0.8345 (ttp) REVERT: F 30 MET cc_start: 0.7428 (tpt) cc_final: 0.7219 (mmm) REVERT: N 24 MET cc_start: 0.8875 (mmm) cc_final: 0.8445 (mmm) REVERT: O 45 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7233 (mt-10) REVERT: T 19 LEU cc_start: 0.7695 (OUTLIER) cc_final: 0.7480 (tp) REVERT: W 24 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7395 (mmm) REVERT: W 27 LEU cc_start: 0.7736 (tt) cc_final: 0.7322 (tm) REVERT: W 31 SER cc_start: 0.8276 (m) cc_final: 0.7958 (m) REVERT: W 43 ILE cc_start: 0.8128 (OUTLIER) cc_final: 0.7903 (mp) REVERT: Z 24 MET cc_start: 0.5175 (mmm) cc_final: 0.4468 (mtp) REVERT: X 67 ILE cc_start: 0.7375 (OUTLIER) cc_final: 0.7082 (pp) outliers start: 54 outliers final: 30 residues processed: 232 average time/residue: 1.2485 time to fit residues: 327.4531 Evaluate side-chains 229 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 193 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 24 MET Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 19 optimal weight: 7.9990 chunk 96 optimal weight: 4.9990 chunk 123 optimal weight: 0.9980 chunk 95 optimal weight: 0.7980 chunk 142 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 168 optimal weight: 8.9990 chunk 105 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 104 optimal weight: 0.7980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19527 Z= 0.230 Angle : 0.699 15.902 26696 Z= 0.274 Chirality : 0.040 0.450 2667 Planarity : 0.003 0.040 3163 Dihedral : 17.859 179.614 4586 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.16 % Allowed : 11.19 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.12 (0.19), residues: 1789 helix: 2.11 (0.14), residues: 1163 sheet: -0.70 (1.10), residues: 24 loop : 0.17 (0.26), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP X 22 HIS 0.011 0.001 HIS L 153 PHE 0.024 0.001 PHE H 20 TYR 0.012 0.002 TYR I 41 ARG 0.005 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 200 time to evaluate : 1.918 Fit side-chains REVERT: M 100 GLU cc_start: 0.7402 (OUTLIER) cc_final: 0.7189 (pm20) REVERT: M 218 MET cc_start: 0.8955 (mtp) cc_final: 0.8526 (mtp) REVERT: D 45 GLU cc_start: 0.7039 (mm-30) cc_final: 0.6770 (mm-30) REVERT: N 24 MET cc_start: 0.8880 (mmm) cc_final: 0.8461 (mmm) REVERT: O 45 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: T 19 LEU cc_start: 0.7714 (OUTLIER) cc_final: 0.7498 (tp) REVERT: W 24 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7382 (mmm) REVERT: W 27 LEU cc_start: 0.7736 (tt) cc_final: 0.7312 (tm) REVERT: W 31 SER cc_start: 0.8266 (m) cc_final: 0.7958 (m) REVERT: W 43 ILE cc_start: 0.8121 (OUTLIER) cc_final: 0.7902 (mp) REVERT: Z 24 MET cc_start: 0.5028 (mmm) cc_final: 0.4403 (mtp) REVERT: X 67 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.7060 (pp) outliers start: 48 outliers final: 26 residues processed: 227 average time/residue: 1.2466 time to fit residues: 319.6859 Evaluate side-chains 227 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 195 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 9 MET Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 24 MET Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 67 optimal weight: 0.0170 chunk 100 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 83 optimal weight: 7.9990 chunk 15 optimal weight: 5.9990 chunk 132 optimal weight: 0.2980 chunk 153 optimal weight: 0.9980 overall best weight: 1.4622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 19527 Z= 0.194 Angle : 0.665 16.116 26696 Z= 0.260 Chirality : 0.039 0.492 2667 Planarity : 0.003 0.039 3163 Dihedral : 17.278 179.696 4586 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.83 % Allowed : 11.72 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.29 (0.19), residues: 1789 helix: 2.28 (0.14), residues: 1161 sheet: -0.50 (1.15), residues: 24 loop : 0.16 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP X 22 HIS 0.010 0.001 HIS L 153 PHE 0.022 0.001 PHE H 20 TYR 0.013 0.001 TYR K 5 ARG 0.007 0.000 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 200 time to evaluate : 1.683 Fit side-chains REVERT: M 100 GLU cc_start: 0.7427 (OUTLIER) cc_final: 0.7180 (pm20) REVERT: D 45 GLU cc_start: 0.7038 (mm-30) cc_final: 0.6780 (mm-30) REVERT: I 52 ASN cc_start: 0.8185 (m110) cc_final: 0.7960 (m110) REVERT: N 24 MET cc_start: 0.8870 (mmm) cc_final: 0.8478 (mmm) REVERT: O 45 GLU cc_start: 0.7489 (OUTLIER) cc_final: 0.7235 (mt-10) REVERT: T 19 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7483 (tp) REVERT: W 24 MET cc_start: 0.7657 (OUTLIER) cc_final: 0.7357 (mmm) REVERT: W 27 LEU cc_start: 0.7760 (tt) cc_final: 0.7330 (tm) REVERT: W 31 SER cc_start: 0.8267 (m) cc_final: 0.7952 (m) REVERT: W 43 ILE cc_start: 0.8115 (OUTLIER) cc_final: 0.7891 (mp) REVERT: Z 24 MET cc_start: 0.4992 (mmm) cc_final: 0.4026 (ttp) REVERT: X 67 ILE cc_start: 0.7379 (OUTLIER) cc_final: 0.7073 (pp) outliers start: 43 outliers final: 27 residues processed: 230 average time/residue: 1.2746 time to fit residues: 331.2691 Evaluate side-chains 228 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 195 time to evaluate : 1.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 24 MET Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 161 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 157 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 123 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 142 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN I 20 GLN N 17 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 19527 Z= 0.417 Angle : 0.863 18.113 26696 Z= 0.340 Chirality : 0.047 0.473 2667 Planarity : 0.004 0.043 3163 Dihedral : 18.510 179.341 4586 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.90 % Allowed : 11.78 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 1.59 (0.19), residues: 1789 helix: 1.69 (0.14), residues: 1155 sheet: -1.08 (1.06), residues: 24 loop : 0.02 (0.26), residues: 610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP X 22 HIS 0.013 0.002 HIS L 153 PHE 0.032 0.002 PHE H 20 TYR 0.018 0.002 TYR I 5 ARG 0.006 0.001 ARG H 202 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 197 time to evaluate : 1.697 Fit side-chains REVERT: M 100 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7218 (pm20) REVERT: D 45 GLU cc_start: 0.7108 (mm-30) cc_final: 0.6833 (mm-30) REVERT: O 45 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7319 (mt-10) REVERT: T 19 LEU cc_start: 0.7713 (OUTLIER) cc_final: 0.7492 (tp) REVERT: W 27 LEU cc_start: 0.7754 (tt) cc_final: 0.7347 (tm) REVERT: W 31 SER cc_start: 0.8373 (m) cc_final: 0.8096 (m) REVERT: W 43 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7881 (mp) REVERT: Z 24 MET cc_start: 0.5242 (mmm) cc_final: 0.4508 (mtp) REVERT: X 67 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7078 (pp) outliers start: 44 outliers final: 30 residues processed: 226 average time/residue: 1.2267 time to fit residues: 313.0252 Evaluate side-chains 229 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 194 time to evaluate : 1.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 38 THR Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain L residue 268 LYS Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 216 PHE Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain P residue 21 SER Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain R residue 35 ILE Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain T residue 25 SER Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 33 LEU Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 166 optimal weight: 10.0000 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 160 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 85 optimal weight: 6.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 17 GLN ** N 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19527 Z= 0.178 Angle : 0.662 16.247 26696 Z= 0.260 Chirality : 0.039 0.513 2667 Planarity : 0.003 0.038 3163 Dihedral : 17.222 179.748 4586 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.24 % Allowed : 12.44 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.23 (0.19), residues: 1789 helix: 2.24 (0.14), residues: 1161 sheet: -0.61 (1.13), residues: 24 loop : 0.12 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP X 22 HIS 0.009 0.001 HIS L 153 PHE 0.021 0.001 PHE H 20 TYR 0.014 0.001 TYR I 5 ARG 0.007 0.000 ARG H 202 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3578 Ramachandran restraints generated. 1789 Oldfield, 0 Emsley, 1789 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 202 time to evaluate : 1.679 Fit side-chains REVERT: M 100 GLU cc_start: 0.7412 (OUTLIER) cc_final: 0.7177 (pm20) REVERT: D 45 GLU cc_start: 0.7011 (mm-30) cc_final: 0.6735 (mm-30) REVERT: G 42 TYR cc_start: 0.8882 (t80) cc_final: 0.8559 (t80) REVERT: N 24 MET cc_start: 0.8880 (mmm) cc_final: 0.8491 (mmm) REVERT: O 45 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7278 (mt-10) REVERT: T 19 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7482 (tp) REVERT: W 27 LEU cc_start: 0.7739 (tt) cc_final: 0.7303 (tm) REVERT: W 31 SER cc_start: 0.8243 (m) cc_final: 0.7938 (m) REVERT: W 43 ILE cc_start: 0.8120 (OUTLIER) cc_final: 0.7901 (mp) REVERT: Z 24 MET cc_start: 0.4993 (mmm) cc_final: 0.4047 (ttp) REVERT: X 67 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.7096 (pp) outliers start: 34 outliers final: 24 residues processed: 224 average time/residue: 1.2163 time to fit residues: 308.2945 Evaluate side-chains 230 residues out of total 1522 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 201 time to evaluate : 1.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 54 VAL Chi-restraints excluded: chain L residue 210 ASP Chi-restraints excluded: chain L residue 260 VAL Chi-restraints excluded: chain M residue 8 THR Chi-restraints excluded: chain M residue 18 LEU Chi-restraints excluded: chain M residue 21 THR Chi-restraints excluded: chain M residue 100 GLU Chi-restraints excluded: chain M residue 142 MET Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 105 MET Chi-restraints excluded: chain H residue 158 LEU Chi-restraints excluded: chain H residue 210 SER Chi-restraints excluded: chain B residue 12 THR Chi-restraints excluded: chain I residue 38 THR Chi-restraints excluded: chain N residue 13 ASP Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain O residue 45 GLU Chi-restraints excluded: chain Q residue 33 LEU Chi-restraints excluded: chain R residue 13 ASP Chi-restraints excluded: chain R residue 21 SER Chi-restraints excluded: chain S residue 29 VAL Chi-restraints excluded: chain T residue 19 LEU Chi-restraints excluded: chain V residue 37 SER Chi-restraints excluded: chain W residue 39 LEU Chi-restraints excluded: chain W residue 43 ILE Chi-restraints excluded: chain Y residue 34 ILE Chi-restraints excluded: chain 1 residue 29 VAL Chi-restraints excluded: chain X residue 67 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 175 random chunks: chunk 147 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 128 optimal weight: 0.7980 chunk 20 optimal weight: 0.0770 chunk 38 optimal weight: 0.0770 chunk 139 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 142 optimal weight: 2.9990 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 15 GLN E 17 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.138886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.107347 restraints weight = 28218.498| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.49 r_work: 0.2896 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2756 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2756 r_free = 0.2756 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2756 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19527 Z= 0.147 Angle : 0.624 16.300 26696 Z= 0.243 Chirality : 0.037 0.484 2667 Planarity : 0.003 0.040 3163 Dihedral : 16.096 179.971 4586 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.04 % Allowed : 12.44 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.57 % 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: 2.56 (0.19), residues: 1789 helix: 2.53 (0.14), residues: 1162 sheet: -0.30 (1.17), residues: 24 loop : 0.16 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP M 148 HIS 0.008 0.001 HIS L 153 PHE 0.019 0.001 PHE L 216 TYR 0.016 0.001 TYR K 5 ARG 0.008 0.000 ARG H 202 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6047.36 seconds wall clock time: 108 minutes 25.11 seconds (6505.11 seconds total)