Starting phenix.real_space_refine on Tue Apr 9 17:25:58 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goc_34175/04_2024/8goc_34175_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goc_34175/04_2024/8goc_34175.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goc_34175/04_2024/8goc_34175.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goc_34175/04_2024/8goc_34175.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goc_34175/04_2024/8goc_34175_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8goc_34175/04_2024/8goc_34175_updated.pdb" } resolution = 4.18 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= 0.010 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: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 36 5.16 5 C 10723 2.51 5 N 2888 2.21 5 O 3280 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 30": "OD1" <-> "OD2" Residue "A ASP 45": "OD1" <-> "OD2" Residue "A TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 144": "OD1" <-> "OD2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 241": "OD1" <-> "OD2" Residue "A TYR 322": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 30": "OD1" <-> "OD2" Residue "B TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 144": "OD1" <-> "OD2" Residue "B GLU 146": "OE1" <-> "OE2" Residue "B TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 339": "OE1" <-> "OE2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C TYR 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 144": "OD1" <-> "OD2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C TYR 239": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 339": "OE1" <-> "OE2" Residue "D TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 154": "OD1" <-> "OD2" Residue "E TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 144": "OE1" <-> "OE2" Residue "H TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 82": "OE1" <-> "OE2" Residue "L TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 154": "OD1" <-> "OD2" Residue "N TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 82": "OE1" <-> "OE2" Residue "N TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 188": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16942 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2725 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 2725 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2725 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 344, 2717 Classifications: {'peptide': 344} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 24, 'TRANS': 316} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "G" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "H" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "M" Number of atoms: 1479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1479 Classifications: {'peptide': 202} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 9, 'TRANS': 189} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "N" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1359 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PCIS': 3, 'PTRANS': 7, 'TRANS': 174} Chain breaks: 1 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 50 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "U" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "V" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 87 Classifications: {'peptide': 10} Link IDs: {'TRANS': 9} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Time building chain proxies: 8.97, per 1000 atoms: 0.53 Number of scatterers: 16942 At special positions: 0 Unit cell: (187.78, 178.76, 96.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 15 15.00 O 3280 8.00 N 2888 7.00 C 10723 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 99 " distance=2.04 Simple disulfide: pdb=" SG CYS D 150 " - pdb=" SG CYS D 206 " distance=2.03 Simple disulfide: pdb=" SG CYS E 24 " - pdb=" SG CYS E 89 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.04 Simple disulfide: pdb=" SG CYS H 150 " - pdb=" SG CYS H 206 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS M 25 " - pdb=" SG CYS M 99 " distance=2.04 Simple disulfide: pdb=" SG CYS M 150 " - pdb=" SG CYS M 206 " distance=2.03 Simple disulfide: pdb=" SG CYS N 24 " - pdb=" SG CYS N 89 " distance=2.03 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 Time building additional restraints: 6.96 Conformation dependent library (CDL) restraints added in 3.3 seconds 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4182 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 18 helices and 43 sheets defined 4.1% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.57 Creating SS restraints... Processing helix chain 'A' and resid 46 through 49 No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'B' and resid 46 through 49 No H-bonds generated for 'chain 'B' and resid 46 through 49' Processing helix chain 'B' and resid 100 through 109 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 100 through 109 Processing helix chain 'D' and resid 65 through 67 No H-bonds generated for 'chain 'D' and resid 65 through 67' Processing helix chain 'D' and resid 91 through 93 No H-bonds generated for 'chain 'D' and resid 91 through 93' Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 184 through 188 Processing helix chain 'H' and resid 65 through 67 No H-bonds generated for 'chain 'H' and resid 65 through 67' Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'L' and resid 123 through 128 Processing helix chain 'L' and resid 184 through 188 Processing helix chain 'M' and resid 65 through 67 No H-bonds generated for 'chain 'M' and resid 65 through 67' Processing helix chain 'M' and resid 91 through 93 No H-bonds generated for 'chain 'M' and resid 91 through 93' Processing helix chain 'N' and resid 123 through 128 Processing helix chain 'N' and resid 184 through 188 Processing sheet with id= A, first strand: chain 'A' and resid 10 through 13 removed outlier: 3.738A pdb=" N PHE A 10 " --> pdb=" O LEU A 23 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 27 through 30 removed outlier: 6.571A pdb=" N ARG A 170 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N ASP A 30 " --> pdb=" O ARG A 170 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 172 " --> pdb=" O ASP A 30 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 165 through 167 removed outlier: 7.009A pdb=" N VAL A 56 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N GLN A 86 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU A 58 " --> pdb=" O ASN A 84 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ASN A 84 " --> pdb=" O LEU A 58 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N VAL A 60 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ILE A 82 " --> pdb=" O VAL A 60 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 128 through 130 Processing sheet with id= E, first strand: chain 'A' and resid 184 through 190 Processing sheet with id= F, first strand: chain 'A' and resid 336 through 342 removed outlier: 3.680A pdb=" N VAL A 336 " --> pdb=" O LEU A 328 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N TYR A 322 " --> pdb=" O PHE A 342 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 232 " --> pdb=" O GLN A 259 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN A 259 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N ALA A 255 " --> pdb=" O VAL A 236 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLN A 238 " --> pdb=" O PRO A 253 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ALA A 240 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N LYS A 251 " --> pdb=" O ALA A 240 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 242 " --> pdb=" O GLN A 249 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N GLN A 249 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 10 through 13 removed outlier: 3.684A pdb=" N PHE B 10 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLY B 40 " --> pdb=" O PHE B 116 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 27 through 29 removed outlier: 6.570A pdb=" N ARG B 170 " --> pdb=" O PHE B 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'B' and resid 165 through 167 removed outlier: 7.017A pdb=" N VAL B 56 " --> pdb=" O GLN B 86 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLN B 86 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N LEU B 58 " --> pdb=" O ASN B 84 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ASN B 84 " --> pdb=" O LEU B 58 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL B 60 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ILE B 82 " --> pdb=" O VAL B 60 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 128 through 130 Processing sheet with id= K, first strand: chain 'B' and resid 184 through 190 Processing sheet with id= L, first strand: chain 'B' and resid 336 through 342 removed outlier: 3.723A pdb=" N VAL B 336 " --> pdb=" O LEU B 328 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N TYR B 322 " --> pdb=" O PHE B 342 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ILE B 232 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLN B 259 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ALA B 255 " --> pdb=" O VAL B 236 " (cutoff:3.500A) removed outlier: 6.026A pdb=" N GLN B 238 " --> pdb=" O PRO B 253 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ALA B 240 " --> pdb=" O LYS B 251 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N LYS B 251 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N ILE B 242 " --> pdb=" O GLN B 249 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N GLN B 249 " --> pdb=" O ILE B 242 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 10 through 13 removed outlier: 3.669A pdb=" N PHE C 10 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLY C 40 " --> pdb=" O PHE C 116 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'C' and resid 27 through 29 removed outlier: 6.373A pdb=" N ARG C 170 " --> pdb=" O PHE C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'C' and resid 165 through 167 removed outlier: 6.942A pdb=" N VAL C 56 " --> pdb=" O GLN C 86 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLN C 86 " --> pdb=" O VAL C 56 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N LEU C 58 " --> pdb=" O ASN C 84 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASN C 84 " --> pdb=" O LEU C 58 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N VAL C 60 " --> pdb=" O ILE C 82 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE C 82 " --> pdb=" O VAL C 60 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'C' and resid 128 through 130 Processing sheet with id= Q, first strand: chain 'C' and resid 184 through 190 Processing sheet with id= R, first strand: chain 'C' and resid 247 through 249 removed outlier: 6.666A pdb=" N VAL C 329 " --> pdb=" O LYS C 230 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ILE C 232 " --> pdb=" O LYS C 327 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N LYS C 327 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL C 234 " --> pdb=" O LYS C 325 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS C 325 " --> pdb=" O VAL C 234 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N VAL C 236 " --> pdb=" O ARG C 323 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ARG C 323 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLN C 238 " --> pdb=" O SER C 321 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N SER C 321 " --> pdb=" O GLN C 238 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA C 240 " --> pdb=" O LEU C 319 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N LEU C 319 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N TYR C 322 " --> pdb=" O PHE C 342 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL C 336 " --> pdb=" O LEU C 328 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'C' and resid 232 through 238 removed outlier: 3.810A pdb=" N ILE C 232 " --> pdb=" O GLN C 259 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLN C 259 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ALA C 255 " --> pdb=" O VAL C 236 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLN C 238 " --> pdb=" O PRO C 253 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 6 through 10 removed outlier: 3.679A pdb=" N SER D 28 " --> pdb=" O GLN D 6 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA D 82 " --> pdb=" O CYS D 25 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'D' and resid 13 through 15 removed outlier: 3.694A pdb=" N GLY D 13 " --> pdb=" O LEU D 118 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA D 52 " --> pdb=" O TRP D 39 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N ARG D 41 " --> pdb=" O TRP D 50 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N TRP D 50 " --> pdb=" O ARG D 41 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'D' and resid 130 through 134 removed outlier: 3.785A pdb=" N SER D 130 " --> pdb=" O LYS D 153 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS D 153 " --> pdb=" O SER D 130 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER D 189 " --> pdb=" O PHE D 176 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'D' and resid 161 through 163 Processing sheet with id= X, first strand: chain 'E' and resid 5 through 8 removed outlier: 3.575A pdb=" N VAL E 20 " --> pdb=" O ILE E 76 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 11 through 14 removed outlier: 5.843A pdb=" N LYS E 104 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 7.395A pdb=" N ALA E 14 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N GLU E 106 " --> pdb=" O ALA E 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'E' and resid 86 through 91 removed outlier: 3.596A pdb=" N THR E 86 " --> pdb=" O GLN E 39 " (cutoff:3.500A) removed outlier: 5.799A pdb=" N GLN E 38 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N LEU E 47 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'E' and resid 115 through 119 removed outlier: 3.554A pdb=" N SER E 115 " --> pdb=" O ASN E 138 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ASN E 138 " --> pdb=" O SER E 115 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL E 134 " --> pdb=" O PHE E 119 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N TYR E 174 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.744A pdb=" N SER H 28 " --> pdb=" O GLN H 6 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU H 84 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N CYS H 25 " --> pdb=" O ALA H 82 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA H 82 " --> pdb=" O CYS H 25 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 13 through 15 removed outlier: 3.753A pdb=" N GLY H 13 " --> pdb=" O LEU H 118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL H 40 " --> pdb=" O TYR H 98 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 130 through 134 removed outlier: 3.671A pdb=" N SER H 130 " --> pdb=" O LYS H 153 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER H 189 " --> pdb=" O PHE H 176 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 161 through 163 Processing sheet with id= AF, first strand: chain 'L' and resid 5 through 8 removed outlier: 3.554A pdb=" N THR L 23 " --> pdb=" O SER L 8 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL L 20 " --> pdb=" O ILE L 76 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'L' and resid 11 through 14 removed outlier: 5.796A pdb=" N LYS L 104 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N ALA L 14 " --> pdb=" O LYS L 104 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N GLU L 106 " --> pdb=" O ALA L 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'L' and resid 86 through 91 removed outlier: 3.732A pdb=" N THR L 86 " --> pdb=" O GLN L 39 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'L' and resid 115 through 119 removed outlier: 3.652A pdb=" N SER L 115 " --> pdb=" O ASN L 138 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN L 138 " --> pdb=" O SER L 115 " (cutoff:3.500A) removed outlier: 5.826A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'M' and resid 6 through 10 removed outlier: 3.750A pdb=" N SER M 28 " --> pdb=" O GLN M 6 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'M' and resid 13 through 15 removed outlier: 3.723A pdb=" N GLY M 13 " --> pdb=" O LEU M 118 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ARG M 41 " --> pdb=" O TRP M 50 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N TRP M 50 " --> pdb=" O ARG M 41 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'M' and resid 130 through 134 removed outlier: 3.657A pdb=" N SER M 130 " --> pdb=" O LYS M 153 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TYR M 186 " --> pdb=" O ASP M 154 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N SER M 189 " --> pdb=" O PHE M 176 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'M' and resid 161 through 163 Processing sheet with id= AN, first strand: chain 'N' and resid 5 through 8 removed outlier: 3.518A pdb=" N THR N 23 " --> pdb=" O SER N 8 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'N' and resid 11 through 14 removed outlier: 5.720A pdb=" N LYS N 104 " --> pdb=" O LEU N 12 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ALA N 14 " --> pdb=" O LYS N 104 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N GLU N 106 " --> pdb=" O ALA N 14 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'N' and resid 86 through 91 removed outlier: 3.709A pdb=" N THR N 86 " --> pdb=" O GLN N 39 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 49 " --> pdb=" O TRP N 36 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N GLN N 38 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU N 47 " --> pdb=" O GLN N 38 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'N' and resid 115 through 119 removed outlier: 3.709A pdb=" N SER N 115 " --> pdb=" O ASN N 138 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASN N 138 " --> pdb=" O SER N 115 " (cutoff:3.500A) removed outlier: 5.803A pdb=" N TYR N 174 " --> pdb=" O ASN N 139 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1410 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.04 Time building geometry restraints manager: 7.42 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: 5430 1.34 - 1.46: 3951 1.46 - 1.58: 7858 1.58 - 1.70: 51 1.70 - 1.82: 48 Bond restraints: 17338 Sorted by residual: bond pdb=" OG1 TPO G 359 " pdb=" P TPO G 359 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" OG1 TPO U 359 " pdb=" P TPO U 359 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" OG1 TPO G 360 " pdb=" P TPO G 360 " ideal model delta sigma weight residual 1.717 1.618 0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.618 0.099 2.00e-02 2.50e+03 2.43e+01 ... (remaining 17333 not shown) Histogram of bond angle deviations from ideal: 97.89 - 105.41: 435 105.41 - 112.92: 9545 112.92 - 120.44: 6189 120.44 - 127.95: 7340 127.95 - 135.47: 125 Bond angle restraints: 23634 Sorted by residual: angle pdb=" CB TPO V 359 " pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 119.31 106.35 12.96 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CB TPO U 359 " pdb=" OG1 TPO U 359 " pdb=" P TPO U 359 " ideal model delta sigma weight residual 119.31 106.36 12.95 3.00e+00 1.11e-01 1.86e+01 angle pdb=" CB TPO G 359 " pdb=" OG1 TPO G 359 " pdb=" P TPO G 359 " ideal model delta sigma weight residual 119.31 106.37 12.94 3.00e+00 1.11e-01 1.86e+01 angle pdb=" C LEU C 49 " pdb=" N LYS C 50 " pdb=" CA LYS C 50 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C LEU B 49 " pdb=" N LYS B 50 " pdb=" CA LYS B 50 " ideal model delta sigma weight residual 121.54 129.01 -7.47 1.91e+00 2.74e-01 1.53e+01 ... (remaining 23629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 9513 17.98 - 35.97: 752 35.97 - 53.95: 98 53.95 - 71.94: 20 71.94 - 89.92: 20 Dihedral angle restraints: 10403 sinusoidal: 3920 harmonic: 6483 Sorted by residual: dihedral pdb=" CA PRO B 95 " pdb=" C PRO B 95 " pdb=" N ARG B 96 " pdb=" CA ARG B 96 " ideal model delta harmonic sigma weight residual 0.00 -38.65 38.65 0 5.00e+00 4.00e-02 5.98e+01 dihedral pdb=" CA PRO C 95 " pdb=" C PRO C 95 " pdb=" N ARG C 96 " pdb=" CA ARG C 96 " ideal model delta harmonic sigma weight residual 0.00 -36.09 36.09 0 5.00e+00 4.00e-02 5.21e+01 dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N ARG A 96 " pdb=" CA ARG A 96 " ideal model delta harmonic sigma weight residual 0.00 -35.56 35.56 0 5.00e+00 4.00e-02 5.06e+01 ... (remaining 10400 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1762 0.036 - 0.072: 567 0.072 - 0.108: 268 0.108 - 0.144: 79 0.144 - 0.179: 12 Chirality restraints: 2688 Sorted by residual: chirality pdb=" CA LYS C 295 " pdb=" N LYS C 295 " pdb=" C LYS C 295 " pdb=" CB LYS C 295 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 8.05e-01 chirality pdb=" CB TPO U 360 " pdb=" CA TPO U 360 " pdb=" OG1 TPO U 360 " pdb=" CG2 TPO U 360 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" CB TPO V 360 " pdb=" CA TPO V 360 " pdb=" OG1 TPO V 360 " pdb=" CG2 TPO V 360 " both_signs ideal model delta sigma weight residual False 2.48 2.31 0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 2685 not shown) Planarity restraints: 3026 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 39 " -0.021 2.00e-02 2.50e+03 1.99e-02 9.94e+00 pdb=" CG TRP H 39 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP H 39 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP H 39 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 39 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 39 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP H 39 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP M 39 " -0.012 2.00e-02 2.50e+03 1.41e-02 5.00e+00 pdb=" CG TRP M 39 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP M 39 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP M 39 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP M 39 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP M 39 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP M 39 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP M 39 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP M 39 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP M 39 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG E 143 " 0.148 9.50e-02 1.11e+02 6.74e-02 4.46e+00 pdb=" NE ARG E 143 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG E 143 " 0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG E 143 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG E 143 " -0.002 2.00e-02 2.50e+03 ... (remaining 3023 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3294 2.78 - 3.31: 16083 3.31 - 3.84: 27085 3.84 - 4.37: 29578 4.37 - 4.90: 52364 Nonbonded interactions: 128404 Sorted by model distance: nonbonded pdb=" O ASN M 31 " pdb=" OG SER M 35 " model vdw 2.249 2.440 nonbonded pdb=" O TYR L 50 " pdb=" OG SER L 54 " model vdw 2.249 2.440 nonbonded pdb=" NZ LYS B 12 " pdb=" O3P TPO U 360 " model vdw 2.253 2.520 nonbonded pdb=" NZ LYS A 12 " pdb=" O3P TPO G 360 " model vdw 2.254 2.520 nonbonded pdb=" NH1 ARG N 62 " pdb=" OD2 ASP N 83 " model vdw 2.257 2.520 ... (remaining 128399 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 7 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 350)) selection = (chain 'B' and (resid 7 through 307 or (resid 308 and (name N or name CA or name \ C or name O or name CB )) or resid 309 through 313 or (resid 314 and (name N or \ name CA or name C or name O or name CB )) or resid 315 through 350)) selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'M' } ncs_group { reference = chain 'E' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'U' selection = chain 'V' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.030 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: 28.170 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 46.980 Find NCS groups from input model: 1.170 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 : 0.004 0.109 17338 Z= 0.293 Angle : 0.746 12.961 23634 Z= 0.367 Chirality : 0.046 0.179 2688 Planarity : 0.004 0.067 3026 Dihedral : 13.289 89.922 6194 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.76 % Favored : 95.05 % Rotamer: Outliers : 0.05 % Allowed : 0.49 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.19), residues: 2163 helix: 1.74 (0.62), residues: 75 sheet: 0.67 (0.17), residues: 945 loop : -0.84 (0.20), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP H 39 HIS 0.004 0.001 HIS B 211 PHE 0.016 0.001 PHE E 140 TYR 0.019 0.001 TYR E 174 ARG 0.023 0.001 ARG E 143 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 191 time to evaluate : 2.036 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 ILE cc_start: 0.8623 (mm) cc_final: 0.8394 (mt) REVERT: E 74 LEU cc_start: 0.8662 (tp) cc_final: 0.8452 (tp) REVERT: E 174 TYR cc_start: 0.8188 (m-80) cc_final: 0.7653 (m-10) REVERT: E 180 LEU cc_start: 0.8428 (tp) cc_final: 0.8177 (tp) REVERT: E 182 LEU cc_start: 0.7721 (mm) cc_final: 0.7501 (mm) REVERT: L 180 LEU cc_start: 0.8348 (tp) cc_final: 0.8021 (tp) REVERT: L 182 LEU cc_start: 0.7942 (mm) cc_final: 0.7736 (mm) REVERT: N 92 TYR cc_start: 0.8813 (p90) cc_final: 0.8548 (p90) REVERT: N 137 LEU cc_start: 0.9105 (mm) cc_final: 0.8780 (mp) REVERT: N 180 LEU cc_start: 0.8535 (tp) cc_final: 0.8318 (tp) REVERT: N 182 LEU cc_start: 0.7938 (mm) cc_final: 0.7723 (mm) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.2613 time to fit residues: 79.3906 Evaluate side-chains 122 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 121 time to evaluate : 2.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 184 optimal weight: 2.9990 chunk 165 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 127 optimal weight: 4.9990 chunk 198 optimal weight: 30.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 102 GLN A 199 HIS ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 282 ASN ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 199 HIS ** C 211 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 GLN ** C 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 167 GLN M 31 ASN M 181 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17338 Z= 0.357 Angle : 0.675 9.852 23634 Z= 0.341 Chirality : 0.045 0.156 2688 Planarity : 0.005 0.058 3026 Dihedral : 6.593 83.442 2430 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.26 % Favored : 92.60 % Rotamer: Outliers : 0.22 % Allowed : 7.37 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.19), residues: 2163 helix: 2.08 (0.65), residues: 72 sheet: 0.40 (0.17), residues: 987 loop : -0.98 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 39 HIS 0.005 0.001 HIS B 211 PHE 0.021 0.002 PHE A 28 TYR 0.013 0.002 TYR L 92 ARG 0.006 0.001 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 2.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8578 (tt) cc_final: 0.8375 (tt) REVERT: A 345 MET cc_start: 0.8324 (ppp) cc_final: 0.7877 (ppp) REVERT: B 120 ILE cc_start: 0.8621 (mm) cc_final: 0.8282 (mt) REVERT: B 275 ILE cc_start: 0.8635 (tt) cc_final: 0.8425 (tt) REVERT: B 345 MET cc_start: 0.8360 (ppp) cc_final: 0.7517 (ppp) REVERT: C 273 TYR cc_start: 0.8734 (m-80) cc_final: 0.8343 (m-10) REVERT: D 39 TRP cc_start: 0.7749 (m100) cc_final: 0.7307 (m100) REVERT: M 39 TRP cc_start: 0.8133 (m100) cc_final: 0.7497 (m100) REVERT: N 92 TYR cc_start: 0.8983 (p90) cc_final: 0.8685 (p90) REVERT: N 162 GLU cc_start: 0.8775 (pp20) cc_final: 0.8470 (tm-30) outliers start: 4 outliers final: 1 residues processed: 160 average time/residue: 0.2664 time to fit residues: 68.3107 Evaluate side-chains 113 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 112 time to evaluate : 1.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 110 optimal weight: 5.9990 chunk 61 optimal weight: 0.3980 chunk 165 optimal weight: 0.9980 chunk 135 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 199 optimal weight: 4.9990 chunk 215 optimal weight: 2.9990 chunk 177 optimal weight: 9.9990 chunk 197 optimal weight: 6.9990 chunk 67 optimal weight: 0.7980 chunk 159 optimal weight: 7.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 199 HIS D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 167 GLN M 31 ASN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 181 GLN ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 17338 Z= 0.228 Angle : 0.607 8.515 23634 Z= 0.302 Chirality : 0.045 0.164 2688 Planarity : 0.004 0.046 3026 Dihedral : 6.342 81.481 2430 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.59 % Favored : 94.27 % Rotamer: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.19), residues: 2163 helix: 1.84 (0.64), residues: 75 sheet: 0.42 (0.17), residues: 1008 loop : -1.04 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 39 HIS 0.004 0.001 HIS C 199 PHE 0.018 0.001 PHE B 145 TYR 0.014 0.001 TYR E 88 ARG 0.005 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 2.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8366 (ppp) cc_final: 0.8054 (ppp) REVERT: B 120 ILE cc_start: 0.8574 (mm) cc_final: 0.8269 (mt) REVERT: C 11 LYS cc_start: 0.8823 (ptmt) cc_final: 0.8307 (ttmt) REVERT: C 273 TYR cc_start: 0.8658 (m-80) cc_final: 0.8262 (m-10) REVERT: D 39 TRP cc_start: 0.7671 (m100) cc_final: 0.7304 (m100) REVERT: D 115 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8014 (tm-30) REVERT: E 174 TYR cc_start: 0.8298 (m-80) cc_final: 0.7825 (m-10) REVERT: L 162 GLU cc_start: 0.9330 (pm20) cc_final: 0.9039 (pm20) REVERT: M 39 TRP cc_start: 0.7983 (m100) cc_final: 0.7507 (m100) REVERT: N 28 GLN cc_start: 0.8437 (tm-30) cc_final: 0.7890 (tm-30) REVERT: N 144 GLU cc_start: 0.9024 (pp20) cc_final: 0.8565 (tp30) REVERT: N 162 GLU cc_start: 0.8776 (pp20) cc_final: 0.8427 (tm-30) REVERT: N 180 LEU cc_start: 0.8486 (pp) cc_final: 0.7538 (tp) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2608 time to fit residues: 72.3026 Evaluate side-chains 119 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 2.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 196 optimal weight: 20.0000 chunk 149 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 chunk 22 optimal weight: 3.9990 chunk 95 optimal weight: 0.0870 chunk 133 optimal weight: 20.0000 chunk 199 optimal weight: 4.9990 chunk 211 optimal weight: 20.0000 chunk 104 optimal weight: 0.9980 chunk 189 optimal weight: 0.9980 chunk 57 optimal weight: 7.9990 overall best weight: 1.6162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 262 GLN D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 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 0.042 17338 Z= 0.276 Angle : 0.615 9.043 23634 Z= 0.308 Chirality : 0.045 0.191 2688 Planarity : 0.004 0.054 3026 Dihedral : 6.439 82.729 2430 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 7.21 % Favored : 92.65 % Rotamer: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.19), residues: 2163 helix: 1.86 (0.64), residues: 75 sheet: 0.34 (0.16), residues: 1008 loop : -1.09 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP H 39 HIS 0.004 0.001 HIS C 199 PHE 0.017 0.002 PHE A 28 TYR 0.012 0.001 TYR E 88 ARG 0.005 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 169 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8525 (tt) cc_final: 0.8319 (tt) REVERT: A 345 MET cc_start: 0.8443 (ppp) cc_final: 0.8209 (ppp) REVERT: B 120 ILE cc_start: 0.8591 (mm) cc_final: 0.8285 (mt) REVERT: B 275 ILE cc_start: 0.8590 (tt) cc_final: 0.8380 (tt) REVERT: C 273 TYR cc_start: 0.8696 (m-80) cc_final: 0.8269 (m-10) REVERT: D 39 TRP cc_start: 0.7739 (m100) cc_final: 0.7321 (m100) REVERT: D 115 GLN cc_start: 0.8625 (tm-30) cc_final: 0.8059 (tm-30) REVERT: E 174 TYR cc_start: 0.8302 (m-80) cc_final: 0.7873 (m-80) REVERT: L 162 GLU cc_start: 0.9359 (pm20) cc_final: 0.9055 (pm20) REVERT: L 180 LEU cc_start: 0.8263 (tp) cc_final: 0.7789 (tp) REVERT: M 39 TRP cc_start: 0.7991 (m100) cc_final: 0.7455 (m100) REVERT: N 144 GLU cc_start: 0.9035 (pp20) cc_final: 0.8582 (tp30) REVERT: N 162 GLU cc_start: 0.8780 (pp20) cc_final: 0.8408 (tm-30) outliers start: 0 outliers final: 0 residues processed: 169 average time/residue: 0.2705 time to fit residues: 72.4470 Evaluate side-chains 119 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 176 optimal weight: 8.9990 chunk 120 optimal weight: 30.0000 chunk 3 optimal weight: 6.9990 chunk 157 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 180 optimal weight: 0.2980 chunk 146 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 108 optimal weight: 2.9990 chunk 190 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 163 ASN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 163 ASN D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17338 Z= 0.253 Angle : 0.620 9.093 23634 Z= 0.305 Chirality : 0.045 0.166 2688 Planarity : 0.004 0.057 3026 Dihedral : 6.363 81.308 2430 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 16.19 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.80 % Favored : 93.11 % Rotamer: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.19), residues: 2163 helix: 1.82 (0.63), residues: 75 sheet: 0.28 (0.16), residues: 1008 loop : -1.08 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP H 39 HIS 0.004 0.001 HIS C 199 PHE 0.015 0.001 PHE A 28 TYR 0.018 0.001 TYR N 92 ARG 0.005 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 2.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8237 (ppp) cc_final: 0.7837 (ppp) REVERT: B 120 ILE cc_start: 0.8572 (mm) cc_final: 0.8283 (mt) REVERT: C 273 TYR cc_start: 0.8701 (m-80) cc_final: 0.8262 (m-10) REVERT: D 39 TRP cc_start: 0.7715 (m100) cc_final: 0.7310 (m100) REVERT: D 115 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8055 (tm-30) REVERT: E 162 GLU cc_start: 0.8839 (pp20) cc_final: 0.8487 (tm-30) REVERT: E 174 TYR cc_start: 0.8292 (m-80) cc_final: 0.7861 (m-80) REVERT: L 162 GLU cc_start: 0.9367 (pm20) cc_final: 0.9082 (pm20) REVERT: L 180 LEU cc_start: 0.8308 (tp) cc_final: 0.7808 (tp) REVERT: M 39 TRP cc_start: 0.7938 (m100) cc_final: 0.7429 (m100) REVERT: N 144 GLU cc_start: 0.9036 (pp20) cc_final: 0.8580 (tp30) REVERT: N 162 GLU cc_start: 0.8793 (pp20) cc_final: 0.8396 (tm-30) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2961 time to fit residues: 80.1034 Evaluate side-chains 120 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 2.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 71 optimal weight: 1.9990 chunk 190 optimal weight: 7.9990 chunk 41 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 211 optimal weight: 8.9990 chunk 175 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 70 optimal weight: 0.3980 chunk 111 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 31 ASN ** D 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN M 31 ASN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17338 Z= 0.279 Angle : 0.625 9.229 23634 Z= 0.311 Chirality : 0.045 0.222 2688 Planarity : 0.004 0.046 3026 Dihedral : 6.447 84.266 2430 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.72 % Favored : 92.23 % Rotamer: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.24 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.58 (0.19), residues: 2163 helix: 1.71 (0.62), residues: 75 sheet: 0.21 (0.16), residues: 1005 loop : -1.10 (0.20), residues: 1083 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP H 39 HIS 0.004 0.001 HIS C 199 PHE 0.017 0.002 PHE C 28 TYR 0.025 0.002 TYR N 92 ARG 0.005 0.000 ARG C 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 2.044 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8510 (tt) cc_final: 0.8282 (tt) REVERT: A 345 MET cc_start: 0.8391 (ppp) cc_final: 0.7853 (ppp) REVERT: B 120 ILE cc_start: 0.8594 (mm) cc_final: 0.8306 (mt) REVERT: B 275 ILE cc_start: 0.8561 (tt) cc_final: 0.8328 (tt) REVERT: C 273 TYR cc_start: 0.8749 (m-80) cc_final: 0.8282 (m-10) REVERT: D 115 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8073 (tm-30) REVERT: E 162 GLU cc_start: 0.8862 (pp20) cc_final: 0.8507 (tm-30) REVERT: E 174 TYR cc_start: 0.8369 (m-80) cc_final: 0.7960 (m-80) REVERT: L 162 GLU cc_start: 0.9360 (pm20) cc_final: 0.9065 (pm20) REVERT: L 180 LEU cc_start: 0.8352 (tp) cc_final: 0.7840 (tp) REVERT: M 39 TRP cc_start: 0.7942 (m100) cc_final: 0.7513 (m100) REVERT: N 92 TYR cc_start: 0.8842 (p90) cc_final: 0.8545 (p90) REVERT: N 144 GLU cc_start: 0.9038 (pp20) cc_final: 0.8482 (tp30) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2673 time to fit residues: 71.4770 Evaluate side-chains 121 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 204 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 120 optimal weight: 30.0000 chunk 154 optimal weight: 9.9990 chunk 119 optimal weight: 3.9990 chunk 178 optimal weight: 8.9990 chunk 118 optimal weight: 30.0000 chunk 211 optimal weight: 30.0000 chunk 132 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN ** H 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 181 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.096 17338 Z= 0.650 Angle : 0.861 9.739 23634 Z= 0.442 Chirality : 0.050 0.230 2688 Planarity : 0.006 0.044 3026 Dihedral : 7.456 89.595 2430 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 25.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 0.05 % Allowed : 4.51 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.29 % 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: -1.11 (0.19), residues: 2163 helix: 1.44 (0.60), residues: 72 sheet: -0.21 (0.17), residues: 1011 loop : -1.38 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP H 39 HIS 0.008 0.002 HIS B 114 PHE 0.037 0.003 PHE C 28 TYR 0.021 0.003 TYR H 60 ARG 0.013 0.001 ARG N 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 140 time to evaluate : 2.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 MET cc_start: 0.8587 (ppp) cc_final: 0.7959 (ppp) REVERT: E 92 TYR cc_start: 0.9187 (p90) cc_final: 0.8881 (p90) REVERT: E 135 CYS cc_start: 0.5597 (p) cc_final: 0.5344 (p) REVERT: E 174 TYR cc_start: 0.8490 (m-80) cc_final: 0.8145 (m-80) REVERT: L 162 GLU cc_start: 0.9355 (pm20) cc_final: 0.9035 (pm20) REVERT: L 180 LEU cc_start: 0.8301 (tp) cc_final: 0.7845 (tp) REVERT: M 39 TRP cc_start: 0.8207 (m100) cc_final: 0.7652 (m100) REVERT: N 144 GLU cc_start: 0.9104 (pp20) cc_final: 0.8550 (tp30) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.2642 time to fit residues: 60.1087 Evaluate side-chains 96 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 96 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 130 optimal weight: 1.9990 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 0.2980 chunk 63 optimal weight: 0.7980 chunk 41 optimal weight: 0.2980 chunk 40 optimal weight: 6.9990 chunk 134 optimal weight: 0.0170 chunk 143 optimal weight: 1.9990 chunk 104 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 31 HIS C 31 HIS D 31 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN H 31 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 31 ASN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN N 167 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17338 Z= 0.185 Angle : 0.649 10.906 23634 Z= 0.316 Chirality : 0.047 0.185 2688 Planarity : 0.004 0.045 3026 Dihedral : 6.484 79.660 2430 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.19), residues: 2163 helix: 1.49 (0.62), residues: 75 sheet: 0.05 (0.17), residues: 1011 loop : -1.14 (0.20), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 39 HIS 0.004 0.001 HIS A 211 PHE 0.015 0.002 PHE E 72 TYR 0.034 0.001 TYR N 92 ARG 0.004 0.000 ARG A 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 1.957 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8548 (tt) cc_final: 0.8340 (tt) REVERT: B 28 PHE cc_start: 0.8406 (m-80) cc_final: 0.8173 (m-80) REVERT: B 120 ILE cc_start: 0.8560 (mm) cc_final: 0.8353 (mt) REVERT: C 273 TYR cc_start: 0.8793 (m-80) cc_final: 0.8298 (m-10) REVERT: D 39 TRP cc_start: 0.7758 (m100) cc_final: 0.7317 (m100) REVERT: E 174 TYR cc_start: 0.8343 (m-80) cc_final: 0.7985 (m-80) REVERT: L 28 GLN cc_start: 0.8328 (tm-30) cc_final: 0.7838 (tm-30) REVERT: L 162 GLU cc_start: 0.9347 (pm20) cc_final: 0.9030 (pm20) REVERT: L 174 TYR cc_start: 0.8163 (m-80) cc_final: 0.7657 (m-80) REVERT: L 180 LEU cc_start: 0.8424 (tp) cc_final: 0.8009 (tp) REVERT: N 144 GLU cc_start: 0.8994 (pp20) cc_final: 0.8494 (tp30) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2499 time to fit residues: 69.7831 Evaluate side-chains 118 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 192 optimal weight: 4.9990 chunk 202 optimal weight: 0.9980 chunk 184 optimal weight: 0.0980 chunk 196 optimal weight: 3.9990 chunk 118 optimal weight: 20.0000 chunk 85 optimal weight: 0.8980 chunk 154 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 177 optimal weight: 6.9990 chunk 186 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN A 282 ASN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 28 GLN E 38 GLN E 125 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** M 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17338 Z= 0.196 Angle : 0.637 10.026 23634 Z= 0.309 Chirality : 0.045 0.162 2688 Planarity : 0.004 0.050 3026 Dihedral : 6.343 78.915 2430 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 0.05 % Allowed : 0.99 % Favored : 98.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.19), residues: 2163 helix: 1.57 (0.62), residues: 75 sheet: 0.16 (0.17), residues: 1002 loop : -1.14 (0.20), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 39 HIS 0.004 0.001 HIS C 199 PHE 0.018 0.001 PHE C 28 TYR 0.022 0.001 TYR N 92 ARG 0.005 0.000 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8514 (tt) cc_final: 0.8293 (tt) REVERT: B 28 PHE cc_start: 0.8403 (m-80) cc_final: 0.8154 (m-80) REVERT: C 273 TYR cc_start: 0.8780 (m-80) cc_final: 0.8294 (m-10) REVERT: D 39 TRP cc_start: 0.7748 (m100) cc_final: 0.7334 (m100) REVERT: E 174 TYR cc_start: 0.8386 (m-80) cc_final: 0.7941 (m-10) REVERT: L 162 GLU cc_start: 0.9346 (pm20) cc_final: 0.9030 (pm20) REVERT: L 174 TYR cc_start: 0.8096 (m-80) cc_final: 0.7585 (m-80) REVERT: L 180 LEU cc_start: 0.8423 (tp) cc_final: 0.7961 (tp) REVERT: N 92 TYR cc_start: 0.8459 (p90) cc_final: 0.7891 (p90) REVERT: N 144 GLU cc_start: 0.9031 (pp20) cc_final: 0.8502 (tp30) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 0.2711 time to fit residues: 71.4455 Evaluate side-chains 116 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 207 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 144 optimal weight: 3.9990 chunk 218 optimal weight: 7.9990 chunk 200 optimal weight: 9.9990 chunk 173 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 134 optimal weight: 0.0570 chunk 106 optimal weight: 0.1980 chunk 138 optimal weight: 0.9990 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 262 GLN D 181 GLN ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN ** M 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17338 Z= 0.193 Angle : 0.627 10.148 23634 Z= 0.302 Chirality : 0.045 0.184 2688 Planarity : 0.004 0.049 3026 Dihedral : 6.188 77.755 2430 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 14.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 0.05 % Allowed : 0.44 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.19), residues: 2163 helix: 1.59 (0.62), residues: 75 sheet: 0.18 (0.16), residues: 1008 loop : -1.10 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP H 39 HIS 0.004 0.001 HIS A 199 PHE 0.015 0.001 PHE N 99 TYR 0.017 0.001 TYR N 92 ARG 0.006 0.000 ARG L 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4326 Ramachandran restraints generated. 2163 Oldfield, 0 Emsley, 2163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 1.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 275 ILE cc_start: 0.8497 (tt) cc_final: 0.8271 (tt) REVERT: B 275 ILE cc_start: 0.8545 (tt) cc_final: 0.8312 (tt) REVERT: C 273 TYR cc_start: 0.8758 (m-80) cc_final: 0.8255 (m-10) REVERT: E 162 GLU cc_start: 0.8750 (pp20) cc_final: 0.8470 (tm-30) REVERT: E 174 TYR cc_start: 0.8410 (m-80) cc_final: 0.7916 (m-10) REVERT: L 162 GLU cc_start: 0.9345 (pm20) cc_final: 0.9027 (pm20) REVERT: L 174 TYR cc_start: 0.7998 (m-80) cc_final: 0.7746 (m-80) REVERT: L 180 LEU cc_start: 0.8399 (tp) cc_final: 0.7930 (tp) REVERT: M 209 ASN cc_start: 0.6592 (m-40) cc_final: 0.6374 (m-40) REVERT: N 92 TYR cc_start: 0.8390 (p90) cc_final: 0.7947 (p90) outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.2770 time to fit residues: 72.0708 Evaluate side-chains 118 residues out of total 1935 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 219 random chunks: chunk 185 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 160 optimal weight: 0.0870 chunk 25 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 174 optimal weight: 20.0000 chunk 72 optimal weight: 6.9990 chunk 178 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 152 optimal weight: 6.9990 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 38 GLN E 125 GLN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 38 GLN ** M 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.100634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.073078 restraints weight = 64389.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073210 restraints weight = 47241.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.074014 restraints weight = 39231.649| |-----------------------------------------------------------------------------| r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17338 Z= 0.263 Angle : 0.651 9.985 23634 Z= 0.317 Chirality : 0.046 0.232 2688 Planarity : 0.004 0.057 3026 Dihedral : 6.319 79.907 2430 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.89 % Cis-general : 0.15 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.19), residues: 2163 helix: 1.61 (0.62), residues: 75 sheet: 0.16 (0.17), residues: 1008 loop : -1.12 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.002 TRP H 39 HIS 0.004 0.001 HIS A 31 PHE 0.021 0.002 PHE N 99 TYR 0.030 0.001 TYR L 92 ARG 0.010 0.000 ARG C 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3496.02 seconds wall clock time: 65 minutes 43.44 seconds (3943.44 seconds total)