Starting phenix.real_space_refine on Thu Nov 16 07:28:41 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8oq7_17107/11_2023/8oq7_17107_updated.pdb" } resolution = 2.2 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 5 5.49 5 S 75 5.16 5 Cl 2 4.86 5 C 9395 2.51 5 N 2215 2.21 5 O 3010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 118": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 14702 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "B" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "D" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "E" Number of atoms: 2731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2731 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 47 Unresolved non-hydrogen angles: 57 Unresolved non-hydrogen dihedrals: 37 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {' CL': 1, 'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 109 Unusual residues: {' CL': 1, 'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 1} Classifications: {'undetermined': 12} Link IDs: {None: 11} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 108 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 108 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 108 Unusual residues: {'D10': 2, 'D12': 2, 'HEX': 3, 'NAG': 2, 'OCT': 1, 'VZA': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "B" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Chain: "C" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 103 Classifications: {'water': 103} Link IDs: {None: 102} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 101 Classifications: {'water': 101} Link IDs: {None: 100} Chain: "E" Number of atoms: 100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 100 Classifications: {'water': 100} Link IDs: {None: 99} Time building chain proxies: 7.91, per 1000 atoms: 0.54 Number of scatterers: 14702 At special positions: 0 Unit cell: (94.15, 94.15, 138.535, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 2 17.00 S 75 16.00 P 5 15.00 O 3010 8.00 N 2215 7.00 C 9395 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=0, symmetry=0 Links applied NAG-ASN " NAG A 602 " - " ASN A 140 " " NAG A 603 " - " ASN A 234 " " NAG B 503 " - " ASN B 140 " " NAG B 504 " - " ASN B 234 " " NAG C 503 " - " ASN C 140 " " NAG C 504 " - " ASN C 234 " " NAG D 503 " - " ASN D 140 " " NAG D 504 " - " ASN D 234 " " NAG E 503 " - " ASN E 140 " " NAG E 504 " - " ASN E 234 " Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 2.6 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 30 sheets defined 38.4% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.84 Creating SS restraints... Processing helix chain 'A' and resid 75 through 77 No H-bonds generated for 'chain 'A' and resid 75 through 77' Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 131 through 133 No H-bonds generated for 'chain 'A' and resid 131 through 133' Processing helix chain 'A' and resid 147 through 152 removed outlier: 3.987A pdb=" N LYS A 151 " --> pdb=" O ARG A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 281 through 304 removed outlier: 4.389A pdb=" N PHE A 290 " --> pdb=" O LEU A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix removed outlier: 3.676A pdb=" N TRP A 300 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL A 301 " --> pdb=" O MET A 297 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER A 302 " --> pdb=" O LEU A 298 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE A 303 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP A 304 " --> pdb=" O TRP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 334 Proline residue: A 315 - end of helix removed outlier: 3.582A pdb=" N SER A 334 " --> pdb=" O GLY A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 379 removed outlier: 3.577A pdb=" N VAL A 359 " --> pdb=" O VAL A 355 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR A 362 " --> pdb=" O SER A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 477 removed outlier: 4.023A pdb=" N ILE A 461 " --> pdb=" O LYS A 457 " (cutoff:3.500A) Proline residue: A 464 - end of helix Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 131 through 133 No H-bonds generated for 'chain 'B' and resid 131 through 133' Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.987A pdb=" N LYS B 151 " --> pdb=" O ARG B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 236 Processing helix chain 'B' and resid 281 through 304 removed outlier: 4.389A pdb=" N PHE B 290 " --> pdb=" O LEU B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.676A pdb=" N TRP B 300 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL B 301 " --> pdb=" O MET B 297 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER B 302 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N PHE B 303 " --> pdb=" O SER B 299 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP B 304 " --> pdb=" O TRP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 334 Proline residue: B 315 - end of helix removed outlier: 3.581A pdb=" N SER B 334 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 379 removed outlier: 3.577A pdb=" N VAL B 359 " --> pdb=" O VAL B 355 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N TYR B 362 " --> pdb=" O SER B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 477 removed outlier: 4.023A pdb=" N ILE B 461 " --> pdb=" O LYS B 457 " (cutoff:3.500A) Proline residue: B 464 - end of helix Processing helix chain 'C' and resid 75 through 77 No H-bonds generated for 'chain 'C' and resid 75 through 77' Processing helix chain 'C' and resid 81 through 83 No H-bonds generated for 'chain 'C' and resid 81 through 83' Processing helix chain 'C' and resid 131 through 133 No H-bonds generated for 'chain 'C' and resid 131 through 133' Processing helix chain 'C' and resid 147 through 152 removed outlier: 3.987A pdb=" N LYS C 151 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 236 Processing helix chain 'C' and resid 281 through 304 removed outlier: 4.389A pdb=" N PHE C 290 " --> pdb=" O LEU C 286 " (cutoff:3.500A) Proline residue: C 291 - end of helix removed outlier: 3.675A pdb=" N TRP C 300 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL C 301 " --> pdb=" O MET C 297 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER C 302 " --> pdb=" O LEU C 298 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N PHE C 303 " --> pdb=" O SER C 299 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP C 304 " --> pdb=" O TRP C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 334 Proline residue: C 315 - end of helix removed outlier: 3.582A pdb=" N SER C 334 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 379 removed outlier: 3.577A pdb=" N VAL C 359 " --> pdb=" O VAL C 355 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR C 362 " --> pdb=" O SER C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 477 removed outlier: 4.023A pdb=" N ILE C 461 " --> pdb=" O LYS C 457 " (cutoff:3.500A) Proline residue: C 464 - end of helix Processing helix chain 'D' and resid 75 through 77 No H-bonds generated for 'chain 'D' and resid 75 through 77' Processing helix chain 'D' and resid 81 through 83 No H-bonds generated for 'chain 'D' and resid 81 through 83' Processing helix chain 'D' and resid 131 through 133 No H-bonds generated for 'chain 'D' and resid 131 through 133' Processing helix chain 'D' and resid 147 through 152 removed outlier: 3.987A pdb=" N LYS D 151 " --> pdb=" O ARG D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 236 Processing helix chain 'D' and resid 281 through 304 removed outlier: 4.389A pdb=" N PHE D 290 " --> pdb=" O LEU D 286 " (cutoff:3.500A) Proline residue: D 291 - end of helix removed outlier: 3.676A pdb=" N TRP D 300 " --> pdb=" O VAL D 296 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N VAL D 301 " --> pdb=" O MET D 297 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER D 302 " --> pdb=" O LEU D 298 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE D 303 " --> pdb=" O SER D 299 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP D 304 " --> pdb=" O TRP D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 334 Proline residue: D 315 - end of helix removed outlier: 3.582A pdb=" N SER D 334 " --> pdb=" O GLY D 330 " (cutoff:3.500A) Processing helix chain 'D' and resid 343 through 379 removed outlier: 3.577A pdb=" N VAL D 359 " --> pdb=" O VAL D 355 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR D 362 " --> pdb=" O SER D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 454 through 477 removed outlier: 4.024A pdb=" N ILE D 461 " --> pdb=" O LYS D 457 " (cutoff:3.500A) Proline residue: D 464 - end of helix Processing helix chain 'E' and resid 75 through 77 No H-bonds generated for 'chain 'E' and resid 75 through 77' Processing helix chain 'E' and resid 81 through 83 No H-bonds generated for 'chain 'E' and resid 81 through 83' Processing helix chain 'E' and resid 131 through 133 No H-bonds generated for 'chain 'E' and resid 131 through 133' Processing helix chain 'E' and resid 147 through 152 removed outlier: 3.987A pdb=" N LYS E 151 " --> pdb=" O ARG E 148 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 236 Processing helix chain 'E' and resid 281 through 304 removed outlier: 4.389A pdb=" N PHE E 290 " --> pdb=" O LEU E 286 " (cutoff:3.500A) Proline residue: E 291 - end of helix removed outlier: 3.676A pdb=" N TRP E 300 " --> pdb=" O VAL E 296 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N VAL E 301 " --> pdb=" O MET E 297 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N SER E 302 " --> pdb=" O LEU E 298 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N PHE E 303 " --> pdb=" O SER E 299 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N TRP E 304 " --> pdb=" O TRP E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 334 Proline residue: E 315 - end of helix removed outlier: 3.581A pdb=" N SER E 334 " --> pdb=" O GLY E 330 " (cutoff:3.500A) Processing helix chain 'E' and resid 343 through 379 removed outlier: 3.577A pdb=" N VAL E 359 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR E 362 " --> pdb=" O SER E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 454 through 477 removed outlier: 4.023A pdb=" N ILE E 461 " --> pdb=" O LYS E 457 " (cutoff:3.500A) Proline residue: E 464 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 226 through 230 removed outlier: 6.315A pdb=" N ILE A 97 " --> pdb=" O MET A 227 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR A 229 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL A 99 " --> pdb=" O TYR A 229 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS A 129 " --> pdb=" O PRO A 98 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N THR A 121 " --> pdb=" O GLU A 106 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU A 108 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR A 119 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 103 through 105 Processing sheet with id= C, first strand: chain 'A' and resid 110 through 112 removed outlier: 3.872A pdb=" N SER A 110 " --> pdb=" O THR A 119 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 158 through 161 removed outlier: 4.630A pdb=" N GLU A 215 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 254 through 262 Processing sheet with id= F, first strand: chain 'A' and resid 163 through 168 removed outlier: 6.994A pdb=" N THR A 195 " --> pdb=" O LYS A 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER A 166 " --> pdb=" O THR A 193 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR A 193 " --> pdb=" O SER A 166 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 226 through 230 removed outlier: 6.315A pdb=" N ILE B 97 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR B 229 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL B 99 " --> pdb=" O TYR B 229 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS B 129 " --> pdb=" O PRO B 98 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR B 121 " --> pdb=" O GLU B 106 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU B 108 " --> pdb=" O THR B 119 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N THR B 119 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 103 through 105 Processing sheet with id= I, first strand: chain 'B' and resid 110 through 112 removed outlier: 3.872A pdb=" N SER B 110 " --> pdb=" O THR B 119 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 158 through 161 removed outlier: 4.630A pdb=" N GLU B 215 " --> pdb=" O VAL B 161 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 254 through 262 Processing sheet with id= L, first strand: chain 'B' and resid 163 through 168 removed outlier: 6.993A pdb=" N THR B 195 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N SER B 166 " --> pdb=" O THR B 193 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR B 193 " --> pdb=" O SER B 166 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 226 through 230 removed outlier: 6.315A pdb=" N ILE C 97 " --> pdb=" O MET C 227 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR C 229 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL C 99 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS C 129 " --> pdb=" O PRO C 98 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR C 121 " --> pdb=" O GLU C 106 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU C 108 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR C 119 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= O, first strand: chain 'C' and resid 110 through 112 removed outlier: 3.872A pdb=" N SER C 110 " --> pdb=" O THR C 119 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 158 through 161 removed outlier: 4.630A pdb=" N GLU C 215 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 254 through 262 Processing sheet with id= R, first strand: chain 'C' and resid 163 through 168 removed outlier: 6.994A pdb=" N THR C 195 " --> pdb=" O LYS C 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER C 166 " --> pdb=" O THR C 193 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR C 193 " --> pdb=" O SER C 166 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 226 through 230 removed outlier: 6.315A pdb=" N ILE D 97 " --> pdb=" O MET D 227 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N TYR D 229 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL D 99 " --> pdb=" O TYR D 229 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS D 129 " --> pdb=" O PRO D 98 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR D 121 " --> pdb=" O GLU D 106 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N LEU D 108 " --> pdb=" O THR D 119 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N THR D 119 " --> pdb=" O LEU D 108 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 103 through 105 Processing sheet with id= U, first strand: chain 'D' and resid 110 through 112 removed outlier: 3.872A pdb=" N SER D 110 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 158 through 161 removed outlier: 4.631A pdb=" N GLU D 215 " --> pdb=" O VAL D 161 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 254 through 262 Processing sheet with id= X, first strand: chain 'D' and resid 163 through 168 removed outlier: 6.993A pdb=" N THR D 195 " --> pdb=" O LYS D 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER D 166 " --> pdb=" O THR D 193 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N THR D 193 " --> pdb=" O SER D 166 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 226 through 230 removed outlier: 6.315A pdb=" N ILE E 97 " --> pdb=" O MET E 227 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N TYR E 229 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N VAL E 99 " --> pdb=" O TYR E 229 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N LYS E 129 " --> pdb=" O PRO E 98 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR E 121 " --> pdb=" O GLU E 106 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N LEU E 108 " --> pdb=" O THR E 119 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N THR E 119 " --> pdb=" O LEU E 108 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 103 through 105 Processing sheet with id= AA, first strand: chain 'E' and resid 110 through 112 removed outlier: 3.872A pdb=" N SER E 110 " --> pdb=" O THR E 119 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'E' and resid 158 through 161 removed outlier: 4.630A pdb=" N GLU E 215 " --> pdb=" O VAL E 161 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'E' and resid 254 through 262 Processing sheet with id= AD, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.994A pdb=" N THR E 195 " --> pdb=" O LYS E 164 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N SER E 166 " --> pdb=" O THR E 193 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N THR E 193 " --> pdb=" O SER E 166 " (cutoff:3.500A) 680 hydrogen bonds defined for protein. 1905 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: 4.90 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3762 1.34 - 1.46: 2906 1.46 - 1.58: 7712 1.58 - 1.69: 0 1.69 - 1.81: 150 Bond restraints: 14530 Sorted by residual: bond pdb=" C4 VZA C 502 " pdb=" C5 VZA C 502 " ideal model delta sigma weight residual 1.551 1.342 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4 VZA A 601 " pdb=" C5 VZA A 601 " ideal model delta sigma weight residual 1.551 1.342 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4 VZA D 502 " pdb=" C5 VZA D 502 " ideal model delta sigma weight residual 1.551 1.342 0.209 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4 VZA B 502 " pdb=" C5 VZA B 502 " ideal model delta sigma weight residual 1.551 1.343 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C4 VZA E 502 " pdb=" C5 VZA E 502 " ideal model delta sigma weight residual 1.551 1.343 0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 14525 not shown) Histogram of bond angle deviations from ideal: 98.43 - 105.56: 260 105.56 - 112.68: 7628 112.68 - 119.80: 4926 119.80 - 126.92: 6600 126.92 - 134.04: 211 Bond angle restraints: 19625 Sorted by residual: angle pdb=" C1 VZA B 502 " pdb=" P2 VZA B 502 " pdb=" C4 VZA B 502 " ideal model delta sigma weight residual 109.47 98.43 11.04 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C1 VZA A 601 " pdb=" P2 VZA A 601 " pdb=" C4 VZA A 601 " ideal model delta sigma weight residual 109.47 98.44 11.03 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C1 VZA E 502 " pdb=" P2 VZA E 502 " pdb=" C4 VZA E 502 " ideal model delta sigma weight residual 109.47 98.45 11.02 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C1 VZA D 502 " pdb=" P2 VZA D 502 " pdb=" C4 VZA D 502 " ideal model delta sigma weight residual 109.47 98.46 11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" C1 VZA C 502 " pdb=" P2 VZA C 502 " pdb=" C4 VZA C 502 " ideal model delta sigma weight residual 109.47 98.47 11.00 3.00e+00 1.11e-01 1.34e+01 ... (remaining 19620 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.12: 7950 16.12 - 32.24: 395 32.24 - 48.36: 75 48.36 - 64.48: 25 64.48 - 80.60: 10 Dihedral angle restraints: 8455 sinusoidal: 3440 harmonic: 5015 Sorted by residual: dihedral pdb=" CA TYR D 340 " pdb=" C TYR D 340 " pdb=" N ILE D 341 " pdb=" CA ILE D 341 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.34e+00 dihedral pdb=" CA TYR A 340 " pdb=" C TYR A 340 " pdb=" N ILE A 341 " pdb=" CA ILE A 341 " ideal model delta harmonic sigma weight residual -180.00 -164.72 -15.28 0 5.00e+00 4.00e-02 9.33e+00 dihedral pdb=" CA TYR C 340 " pdb=" C TYR C 340 " pdb=" N ILE C 341 " pdb=" CA ILE C 341 " ideal model delta harmonic sigma weight residual -180.00 -164.76 -15.24 0 5.00e+00 4.00e-02 9.29e+00 ... (remaining 8452 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.295: 2220 0.295 - 0.589: 0 0.589 - 0.884: 5 0.884 - 1.179: 0 1.179 - 1.473: 5 Chirality restraints: 2230 Sorted by residual: chirality pdb=" C1 NAG E 504 " pdb=" ND2 ASN E 234 " pdb=" C2 NAG E 504 " pdb=" O5 NAG E 504 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.43e+01 chirality pdb=" C1 NAG C 504 " pdb=" ND2 ASN C 234 " pdb=" C2 NAG C 504 " pdb=" O5 NAG C 504 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.42e+01 chirality pdb=" C1 NAG A 603 " pdb=" ND2 ASN A 234 " pdb=" C2 NAG A 603 " pdb=" O5 NAG A 603 " both_signs ideal model delta sigma weight residual False -2.40 -0.93 -1.47 2.00e-01 2.50e+01 5.42e+01 ... (remaining 2227 not shown) Planarity restraints: 2365 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 234 " -0.147 2.00e-02 2.50e+03 2.80e-01 9.78e+02 pdb=" CG ASN B 234 " 0.081 2.00e-02 2.50e+03 pdb=" OD1 ASN B 234 " -0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN B 234 " 0.499 2.00e-02 2.50e+03 pdb=" C1 NAG B 504 " -0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN E 234 " -0.147 2.00e-02 2.50e+03 2.80e-01 9.77e+02 pdb=" CG ASN E 234 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN E 234 " -0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN E 234 " 0.499 2.00e-02 2.50e+03 pdb=" C1 NAG E 504 " -0.316 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 234 " -0.147 2.00e-02 2.50e+03 2.80e-01 9.77e+02 pdb=" CG ASN D 234 " 0.082 2.00e-02 2.50e+03 pdb=" OD1 ASN D 234 " -0.117 2.00e-02 2.50e+03 pdb=" ND2 ASN D 234 " 0.499 2.00e-02 2.50e+03 pdb=" C1 NAG D 504 " -0.316 2.00e-02 2.50e+03 ... (remaining 2362 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 3414 2.81 - 3.33: 12997 3.33 - 3.86: 23688 3.86 - 4.38: 29132 4.38 - 4.90: 48897 Nonbonded interactions: 118128 Sorted by model distance: nonbonded pdb=" O PHE D 86 " pdb=" O HOH D 601 " model vdw 2.290 2.440 nonbonded pdb=" O PHE A 86 " pdb=" O HOH A 701 " model vdw 2.290 2.440 nonbonded pdb=" O PHE B 86 " pdb=" O HOH B 601 " model vdw 2.290 2.440 nonbonded pdb=" O PHE E 86 " pdb=" O HOH E 601 " model vdw 2.291 2.440 nonbonded pdb=" O PHE C 86 " pdb=" O HOH C 601 " model vdw 2.291 2.440 ... (remaining 118123 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 74 through 479 or resid 603 or resid 605 through 606)) selection = (chain 'B' and (resid 74 through 479 or resid 503 or resid 505 through 506)) selection = (chain 'C' and (resid 74 through 479 or resid 503 or resid 505 through 506)) selection = (chain 'D' and (resid 74 through 479 or resid 503 or resid 505 through 506)) selection = (chain 'E' and (resid 74 through 479 or resid 503 or resid 505 through 506)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.260 Check model and map are aligned: 0.200 Set scattering table: 0.130 Process input model: 40.140 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 76.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 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 : 0.009 0.209 14530 Z= 0.614 Angle : 0.905 11.035 19625 Z= 0.456 Chirality : 0.092 1.473 2230 Planarity : 0.005 0.038 2355 Dihedral : 10.998 80.605 5195 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 0.33 % Allowed : 2.33 % Favored : 97.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.27 (0.20), residues: 1660 helix: 2.31 (0.22), residues: 565 sheet: 1.67 (0.23), residues: 435 loop : 0.77 (0.23), residues: 660 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 263 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 268 average time/residue: 1.5134 time to fit residues: 438.6035 Evaluate side-chains 225 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 222 time to evaluate : 1.765 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 2.2664 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 0.9990 chunk 125 optimal weight: 0.9990 chunk 69 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 84 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 129 optimal weight: 6.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 chunk 96 optimal weight: 9.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 199 ASN D 251 GLN E 181 GLN E 199 ASN E 251 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14530 Z= 0.217 Angle : 0.628 5.104 19625 Z= 0.352 Chirality : 0.045 0.169 2230 Planarity : 0.004 0.034 2355 Dihedral : 7.426 56.880 2105 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.13 % Allowed : 6.45 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.32 (0.20), residues: 1660 helix: 2.39 (0.22), residues: 560 sheet: 1.59 (0.25), residues: 405 loop : 0.92 (0.23), residues: 695 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 227 time to evaluate : 1.807 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 32 outliers final: 7 residues processed: 237 average time/residue: 1.4869 time to fit residues: 382.2133 Evaluate side-chains 221 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 214 time to evaluate : 1.716 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 2 residues processed: 5 average time/residue: 1.2591 time to fit residues: 9.1433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 83 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 41 optimal weight: 0.0980 chunk 150 optimal weight: 0.7980 chunk 162 optimal weight: 8.9990 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 51 optimal weight: 8.9990 chunk 120 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN C 199 ASN C 251 GLN C 269 ASN D 181 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 269 ASN E 181 GLN E 199 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 14530 Z= 0.200 Angle : 0.596 6.556 19625 Z= 0.333 Chirality : 0.044 0.171 2230 Planarity : 0.004 0.034 2355 Dihedral : 7.332 58.594 2105 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 1.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.46 % Allowed : 7.31 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.42 (0.20), residues: 1660 helix: 2.89 (0.22), residues: 530 sheet: 1.42 (0.24), residues: 425 loop : 0.81 (0.23), residues: 705 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 214 time to evaluate : 1.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 10 residues processed: 228 average time/residue: 1.4930 time to fit residues: 369.7641 Evaluate side-chains 216 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 206 time to evaluate : 1.697 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 1.1000 time to fit residues: 7.1186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 148 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 100 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN B 287 GLN C 199 ASN C 251 GLN D 181 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 251 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 14530 Z= 0.292 Angle : 0.712 5.852 19625 Z= 0.403 Chirality : 0.048 0.222 2230 Planarity : 0.005 0.037 2355 Dihedral : 8.661 59.303 2105 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.59 % Allowed : 7.97 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.10 (0.19), residues: 1660 helix: 2.61 (0.21), residues: 530 sheet: 1.49 (0.26), residues: 345 loop : 0.58 (0.21), residues: 785 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 207 time to evaluate : 1.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 18 residues processed: 222 average time/residue: 1.6016 time to fit residues: 385.2349 Evaluate side-chains 222 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 204 time to evaluate : 1.604 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 11 residues processed: 7 average time/residue: 1.3269 time to fit residues: 12.2220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN B 269 ASN C 199 ASN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 14530 Z= 0.302 Angle : 0.731 6.197 19625 Z= 0.413 Chirality : 0.048 0.184 2230 Planarity : 0.005 0.040 2355 Dihedral : 9.429 58.802 2105 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.12 % Allowed : 7.38 % Favored : 89.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.94 (0.19), residues: 1660 helix: 2.44 (0.21), residues: 530 sheet: 1.42 (0.26), residues: 345 loop : 0.50 (0.21), residues: 785 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 207 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 16 residues processed: 229 average time/residue: 1.6119 time to fit residues: 398.5261 Evaluate side-chains 222 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 206 time to evaluate : 1.651 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 11 residues processed: 5 average time/residue: 1.1074 time to fit residues: 8.3365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 53 optimal weight: 1.9990 chunk 143 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 159 optimal weight: 0.7980 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 287 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 14530 Z= 0.290 Angle : 0.712 6.002 19625 Z= 0.403 Chirality : 0.047 0.180 2230 Planarity : 0.005 0.039 2355 Dihedral : 9.359 59.907 2105 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 1.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.52 % Allowed : 8.57 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 1.92 (0.20), residues: 1660 helix: 2.42 (0.22), residues: 530 sheet: 1.41 (0.26), residues: 345 loop : 0.49 (0.21), residues: 785 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 206 time to evaluate : 1.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 38 outliers final: 16 residues processed: 221 average time/residue: 1.6544 time to fit residues: 394.6208 Evaluate side-chains 220 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 204 time to evaluate : 1.769 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 12 residues processed: 4 average time/residue: 1.1699 time to fit residues: 7.4810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 153 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 134 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 159 optimal weight: 0.9980 chunk 99 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14530 Z= 0.203 Angle : 0.599 5.101 19625 Z= 0.337 Chirality : 0.044 0.168 2230 Planarity : 0.004 0.034 2355 Dihedral : 8.698 59.406 2105 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 1.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.26 % Allowed : 8.77 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.24 (0.20), residues: 1660 helix: 2.64 (0.22), residues: 530 sheet: 1.42 (0.24), residues: 410 loop : 0.74 (0.23), residues: 720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 207 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 15 residues processed: 226 average time/residue: 1.4828 time to fit residues: 363.9014 Evaluate side-chains 220 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.528 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 12 residues processed: 3 average time/residue: 1.2471 time to fit residues: 6.3001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 63 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 101 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 78 optimal weight: 5.9990 chunk 14 optimal weight: 0.6980 chunk 125 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 181 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14530 Z= 0.222 Angle : 0.622 5.335 19625 Z= 0.350 Chirality : 0.045 0.170 2230 Planarity : 0.004 0.035 2355 Dihedral : 8.624 59.188 2105 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.06 % Allowed : 9.57 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.08 (0.20), residues: 1660 helix: 2.62 (0.22), residues: 530 sheet: 1.44 (0.26), residues: 345 loop : 0.58 (0.21), residues: 785 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 1.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 221 average time/residue: 1.5581 time to fit residues: 373.2914 Evaluate side-chains 220 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 205 time to evaluate : 1.639 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 11 residues processed: 4 average time/residue: 1.1618 time to fit residues: 7.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 152 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 148 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 116 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN A 269 ASN B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 0.021 14530 Z= 0.202 Angle : 0.594 5.122 19625 Z= 0.333 Chirality : 0.044 0.169 2230 Planarity : 0.004 0.034 2355 Dihedral : 8.329 59.890 2105 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 1.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.79 % Allowed : 9.83 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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 (0.20), residues: 1660 helix: 2.68 (0.22), residues: 530 sheet: 1.36 (0.26), residues: 355 loop : 0.62 (0.21), residues: 775 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 207 time to evaluate : 1.778 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 13 residues processed: 226 average time/residue: 1.5294 time to fit residues: 375.1424 Evaluate side-chains 219 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 206 time to evaluate : 1.632 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 1.1200 time to fit residues: 5.8353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 156 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 164 optimal weight: 0.9990 chunk 151 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 101 optimal weight: 0.6980 chunk 80 optimal weight: 0.9990 chunk 103 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 14530 Z= 0.197 Angle : 0.587 5.373 19625 Z= 0.329 Chirality : 0.044 0.167 2230 Planarity : 0.004 0.034 2355 Dihedral : 8.064 58.176 2105 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 1.00 % Allowed : 10.83 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.07 (0.20), residues: 1660 helix: 2.72 (0.22), residues: 530 sheet: 1.18 (0.25), residues: 370 loop : 0.60 (0.22), residues: 760 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 206 time to evaluate : 1.603 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 216 average time/residue: 1.5577 time to fit residues: 364.2127 Evaluate side-chains 213 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 203 time to evaluate : 1.656 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 0 time to fit residues: 2.2209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 139 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 120 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 36 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 134 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 115 optimal weight: 0.0470 overall best weight: 1.1082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 181 GLN A 199 ASN A 251 GLN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 181 GLN B 199 ASN B 251 GLN C 199 ASN C 251 GLN D 199 ASN ** D 251 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 181 GLN E 199 ASN E 251 GLN ** E 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.139742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.116367 restraints weight = 11195.547| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 0.87 r_work: 0.3089 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 14530 Z= 0.226 Angle : 0.628 5.868 19625 Z= 0.353 Chirality : 0.045 0.171 2230 Planarity : 0.004 0.035 2355 Dihedral : 8.211 58.518 2105 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.33 % Allowed : 10.56 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.33 % Cis-general : 0.31 % 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: 2.06 (0.20), residues: 1660 helix: 2.63 (0.22), residues: 530 sheet: 1.34 (0.26), residues: 355 loop : 0.56 (0.21), residues: 775 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6337.26 seconds wall clock time: 112 minutes 55.55 seconds (6775.55 seconds total)