Starting phenix.real_space_refine on Sun Jul 21 00:41:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/07_2024/8ut9_42534.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/07_2024/8ut9_42534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/07_2024/8ut9_42534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/07_2024/8ut9_42534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/07_2024/8ut9_42534.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ut9_42534/07_2024/8ut9_42534.cif" } resolution = 3.3 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= 0.016 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: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 7833 2.51 5 N 2266 2.21 5 O 2542 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 163": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12707 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 2422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2422 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 13, 'TRANS': 303} Chain: "B" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "C" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2414 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "D" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "E" Number of atoms: 2414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2414 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 13, 'TRANS': 302} Chain: "F" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Link IDs: {'TRANS': 166} Chain: "G" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 630 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 126} Link IDs: {'TRANS': 125} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 378 Unresolved non-hydrogen dihedrals: 126 Planarities with less than four sites: {'UNK:plan-1': 126} Unresolved non-hydrogen planarities: 126 Chain: "H" Number of atoms: 540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 540 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 108} Link IDs: {'TRANS': 107} Unresolved non-hydrogen bonds: 216 Unresolved non-hydrogen angles: 324 Unresolved non-hydrogen dihedrals: 108 Planarities with less than four sites: {'UNK:plan-1': 108} Unresolved non-hydrogen planarities: 108 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.67, per 1000 atoms: 0.68 Number of scatterers: 12707 At special positions: 0 Unit cell: (83.375, 107.3, 143.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 2542 8.00 N 2266 7.00 C 7833 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 66 " distance=2.04 Simple disulfide: pdb=" SG CYS A 87 " - pdb=" SG CYS A 129 " distance=2.03 Simple disulfide: pdb=" SG CYS A 272 " - pdb=" SG CYS A 296 " distance=2.03 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.05 Simple disulfide: pdb=" SG CYS C 42 " - pdb=" SG CYS C 268 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 66 " distance=2.04 Simple disulfide: pdb=" SG CYS C 87 " - pdb=" SG CYS C 129 " distance=2.05 Simple disulfide: pdb=" SG CYS C 272 " - pdb=" SG CYS C 296 " distance=2.05 Simple disulfide: pdb=" SG CYS D 144 " - pdb=" SG CYS D 148 " distance=2.03 Simple disulfide: pdb=" SG CYS E 4 " - pdb=" SG CYS F 137 " distance=2.03 Simple disulfide: pdb=" SG CYS E 42 " - pdb=" SG CYS E 268 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 66 " distance=2.03 Simple disulfide: pdb=" SG CYS E 87 " - pdb=" SG CYS E 129 " distance=2.03 Simple disulfide: pdb=" SG CYS E 272 " - pdb=" SG CYS E 296 " distance=2.02 Simple disulfide: pdb=" SG CYS F 144 " - pdb=" SG CYS F 148 " distance=2.04 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 BETA1-3 " NAG I 1 " - " NAG I 2 " BETA1-4 " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " NAG-ASN " NAG A 401 " - " ASN A 28 " " NAG A 402 " - " ASN A 231 " " NAG B 301 " - " ASN B 154 " " NAG C 401 " - " ASN C 12 " " NAG C 402 " - " ASN C 28 " " NAG D 301 " - " ASN D 154 " " NAG E 401 " - " ASN E 28 " " NAG E 402 " - " ASN E 231 " " NAG F 301 " - " ASN F 154 " " NAG I 1 " - " ASN B 82 " " NAG J 1 " - " ASN D 82 " " NAG K 1 " - " ASN F 82 " Time building additional restraints: 5.12 Conformation dependent library (CDL) restraints added in 2.1 seconds 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3104 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 38 sheets defined 28.3% alpha, 29.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 removed outlier: 3.642A pdb=" N THR A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 70 removed outlier: 5.700A pdb=" N GLN A 68 " --> pdb=" O GLN A 65 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU A 70 " --> pdb=" O ASP A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 Processing helix chain 'A' and resid 178 through 185 Processing helix chain 'B' and resid 37 through 56 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 146 through 154 removed outlier: 3.977A pdb=" N ALA B 150 " --> pdb=" O ASP B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 164 removed outlier: 4.400A pdb=" N GLU B 164 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 169 removed outlier: 3.569A pdb=" N ASN B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 62 removed outlier: 4.277A pdb=" N THR C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 70 removed outlier: 3.916A pdb=" N ASP C 67 " --> pdb=" O PRO C 64 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N GLN C 68 " --> pdb=" O GLN C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 104 removed outlier: 3.638A pdb=" N GLU C 104 " --> pdb=" O GLN C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 178 through 186 Processing helix chain 'D' and resid 37 through 56 Processing helix chain 'D' and resid 74 through 127 Processing helix chain 'D' and resid 145 through 155 removed outlier: 3.680A pdb=" N MET D 149 " --> pdb=" O ASP D 145 " (cutoff:3.500A) Processing helix chain 'D' and resid 162 through 171 removed outlier: 4.188A pdb=" N ALA D 166 " --> pdb=" O TYR D 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 62 Processing helix chain 'E' and resid 63 through 70 removed outlier: 5.507A pdb=" N GLN E 68 " --> pdb=" O GLN E 65 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 70 " --> pdb=" O ASP E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 94 through 104 Processing helix chain 'E' and resid 178 through 187 Processing helix chain 'F' and resid 38 through 56 Processing helix chain 'F' and resid 74 through 127 Processing helix chain 'F' and resid 145 through 154 Processing helix chain 'F' and resid 162 through 171 Processing helix chain 'G' and resid 61 through 65 removed outlier: 3.666A pdb=" N UNK G 65 " --> pdb=" O UNK G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 74 through 76 No H-bonds generated for 'chain 'G' and resid 74 through 76' Processing helix chain 'G' and resid 87 through 90 Processing helix chain 'G' and resid 109 through 113 removed outlier: 3.604A pdb=" N UNK G 113 " --> pdb=" O UNK G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 32 No H-bonds generated for 'chain 'H' and resid 30 through 32' Processing helix chain 'H' and resid 80 through 84 removed outlier: 3.631A pdb=" N UNK H 84 " --> pdb=" O UNK H 81 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 32 through 36 removed outlier: 3.508A pdb=" N GLN B 27 " --> pdb=" O LYS A 2 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS A 2 " --> pdb=" O GLN B 27 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 34 Processing sheet with id=AA5, first strand: chain 'A' and resid 41 through 42 removed outlier: 6.089A pdb=" N ILE A 41 " --> pdb=" O ASP A 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 48 through 51 Processing sheet with id=AA7, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.729A pdb=" N LYS A 91 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N TRP A 225 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N VAL A 170 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ARG A 247 " --> pdb=" O VAL A 170 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 90 through 92 removed outlier: 6.729A pdb=" N LYS A 91 " --> pdb=" O PHE A 223 " (cutoff:3.500A) removed outlier: 8.787A pdb=" N TRP A 225 " --> pdb=" O LYS A 91 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL A 170 " --> pdb=" O PRO A 245 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 155 through 160 Processing sheet with id=AB1, first strand: chain 'A' and resid 272 through 274 removed outlier: 4.031A pdb=" N CYS A 272 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 31 through 36 removed outlier: 3.805A pdb=" N GLN D 27 " --> pdb=" O LYS C 2 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LYS C 2 " --> pdb=" O GLN D 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 14 through 16 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'C' and resid 33 through 34 Processing sheet with id=AB6, first strand: chain 'C' and resid 41 through 42 removed outlier: 5.695A pdb=" N ILE C 41 " --> pdb=" O ASP C 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 50 removed outlier: 3.744A pdb=" N ILE C 78 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE C 77 " --> pdb=" O ILE C 258 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.889A pdb=" N PHE C 72 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG C 247 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C 170 " --> pdb=" O ARG C 247 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LYS C 91 " --> pdb=" O PHE C 223 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N TRP C 225 " --> pdb=" O LYS C 91 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 72 through 73 removed outlier: 3.889A pdb=" N PHE C 72 " --> pdb=" O ILE C 108 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARG C 247 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N VAL C 170 " --> pdb=" O ARG C 247 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 120 through 121 Processing sheet with id=AC2, first strand: chain 'C' and resid 126 through 130 removed outlier: 3.689A pdb=" N SER C 135 " --> pdb=" O THR C 126 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 155 through 159 Processing sheet with id=AC4, first strand: chain 'C' and resid 272 through 274 removed outlier: 3.879A pdb=" N CYS C 272 " --> pdb=" O ILE C 279 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 14 through 15 removed outlier: 7.842A pdb=" N TRP F 14 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N HIS E 7 " --> pdb=" O TRP F 14 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LYS E 2 " --> pdb=" O GLN F 27 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 14 through 15 removed outlier: 7.842A pdb=" N TRP F 14 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N HIS E 7 " --> pdb=" O TRP F 14 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 14 through 16 Processing sheet with id=AC8, first strand: chain 'E' and resid 29 through 31 Processing sheet with id=AC9, first strand: chain 'E' and resid 33 through 34 Processing sheet with id=AD1, first strand: chain 'E' and resid 41 through 42 removed outlier: 5.469A pdb=" N ILE E 41 " --> pdb=" O ASP E 265 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'E' and resid 48 through 51 removed outlier: 6.666A pdb=" N VAL E 49 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE E 77 " --> pdb=" O ILE E 258 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 90 through 92 removed outlier: 6.716A pdb=" N LYS E 91 " --> pdb=" O PHE E 223 " (cutoff:3.500A) removed outlier: 8.764A pdb=" N TRP E 225 " --> pdb=" O LYS E 91 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N VAL E 170 " --> pdb=" O ARG E 247 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ARG E 247 " --> pdb=" O VAL E 170 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AD5, first strand: chain 'E' and resid 155 through 160 Processing sheet with id=AD6, first strand: chain 'E' and resid 277 through 278 Processing sheet with id=AD7, first strand: chain 'G' and resid 3 through 6 Processing sheet with id=AD8, first strand: chain 'G' and resid 10 through 12 removed outlier: 3.598A pdb=" N UNK G 92 " --> pdb=" O UNK G 123 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N UNK G 33 " --> pdb=" O UNK G 99 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N UNK G 32 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N UNK G 52 " --> pdb=" O UNK G 32 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N UNK G 34 " --> pdb=" O UNK G 50 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N UNK G 50 " --> pdb=" O UNK G 34 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N UNK G 36 " --> pdb=" O UNK G 48 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 4 through 5 Processing sheet with id=AE1, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.655A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N UNK H 38 " --> pdb=" O UNK H 47 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N UNK H 47 " --> pdb=" O UNK H 38 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 10 through 13 removed outlier: 6.655A pdb=" N UNK H 11 " --> pdb=" O UNK H 107 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1455 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: 4.27 Time building geometry restraints manager: 5.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 4373 1.34 - 1.48: 3084 1.48 - 1.61: 5355 1.61 - 1.75: 5 1.75 - 1.88: 92 Bond restraints: 12909 Sorted by residual: bond pdb=" N CYS A 268 " pdb=" CA CYS A 268 " ideal model delta sigma weight residual 1.454 1.493 -0.039 1.17e-02 7.31e+03 1.12e+01 bond pdb=" CA UNK H 67 " pdb=" CB UNK H 67 " ideal model delta sigma weight residual 1.530 1.471 0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" SD MET A 311 " pdb=" CE MET A 311 " ideal model delta sigma weight residual 1.791 1.722 0.069 2.50e-02 1.60e+03 7.65e+00 bond pdb=" CB PRO C 315 " pdb=" CG PRO C 315 " ideal model delta sigma weight residual 1.492 1.628 -0.136 5.00e-02 4.00e+02 7.37e+00 bond pdb=" N LYS B 161 " pdb=" CA LYS B 161 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.85e+00 ... (remaining 12904 not shown) Histogram of bond angle deviations from ideal: 97.30 - 104.63: 141 104.63 - 111.96: 5849 111.96 - 119.29: 4882 119.29 - 126.63: 6453 126.63 - 133.96: 155 Bond angle restraints: 17480 Sorted by residual: angle pdb=" CA PRO C 315 " pdb=" N PRO C 315 " pdb=" CD PRO C 315 " ideal model delta sigma weight residual 112.00 100.59 11.41 1.40e+00 5.10e-01 6.65e+01 angle pdb=" CA CYS C 296 " pdb=" CB CYS C 296 " pdb=" SG CYS C 296 " ideal model delta sigma weight residual 114.40 132.20 -17.80 2.30e+00 1.89e-01 5.99e+01 angle pdb=" N GLU B 164 " pdb=" CA GLU B 164 " pdb=" C GLU B 164 " ideal model delta sigma weight residual 111.33 103.52 7.81 1.21e+00 6.83e-01 4.16e+01 angle pdb=" CA CYS A 42 " pdb=" CB CYS A 42 " pdb=" SG CYS A 42 " ideal model delta sigma weight residual 114.40 128.33 -13.93 2.30e+00 1.89e-01 3.67e+01 angle pdb=" CA CYS F 144 " pdb=" CB CYS F 144 " pdb=" SG CYS F 144 " ideal model delta sigma weight residual 114.40 124.46 -10.06 2.30e+00 1.89e-01 1.91e+01 ... (remaining 17475 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 7301 17.98 - 35.96: 464 35.96 - 53.93: 133 53.93 - 71.91: 42 71.91 - 89.89: 19 Dihedral angle restraints: 7959 sinusoidal: 3137 harmonic: 4822 Sorted by residual: dihedral pdb=" CB CYS D 144 " pdb=" SG CYS D 144 " pdb=" SG CYS D 148 " pdb=" CB CYS D 148 " ideal model delta sinusoidal sigma weight residual -86.00 -172.54 86.54 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CD ARG B 163 " pdb=" NE ARG B 163 " pdb=" CZ ARG B 163 " pdb=" NH1 ARG B 163 " ideal model delta sinusoidal sigma weight residual 0.00 -82.06 82.06 1 1.00e+01 1.00e-02 8.27e+01 dihedral pdb=" CB CYS C 87 " pdb=" SG CYS C 87 " pdb=" SG CYS C 129 " pdb=" CB CYS C 129 " ideal model delta sinusoidal sigma weight residual 93.00 13.54 79.46 1 1.00e+01 1.00e-02 7.84e+01 ... (remaining 7956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1641 0.075 - 0.151: 303 0.151 - 0.226: 30 0.226 - 0.301: 7 0.301 - 0.377: 4 Chirality restraints: 1985 Sorted by residual: chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN B 82 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.02 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CB THR D 49 " pdb=" CA THR D 49 " pdb=" OG1 THR D 49 " pdb=" CG2 THR D 49 " both_signs ideal model delta sigma weight residual False 2.55 2.22 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CA CYS C 296 " pdb=" N CYS C 296 " pdb=" C CYS C 296 " pdb=" CB CYS C 296 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1982 not shown) Planarity restraints: 2327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 163 " 1.089 9.50e-02 1.11e+02 4.88e-01 1.44e+02 pdb=" NE ARG B 163 " -0.065 2.00e-02 2.50e+03 pdb=" CZ ARG B 163 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 163 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG B 163 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL E 314 " -0.097 5.00e-02 4.00e+02 1.45e-01 3.38e+01 pdb=" N PRO E 315 " 0.251 5.00e-02 4.00e+02 pdb=" CA PRO E 315 " -0.080 5.00e-02 4.00e+02 pdb=" CD PRO E 315 " -0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 314 " -0.089 5.00e-02 4.00e+02 1.26e-01 2.55e+01 pdb=" N PRO C 315 " 0.218 5.00e-02 4.00e+02 pdb=" CA PRO C 315 " -0.062 5.00e-02 4.00e+02 pdb=" CD PRO C 315 " -0.066 5.00e-02 4.00e+02 ... (remaining 2324 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.33: 17 2.33 - 2.97: 6042 2.97 - 3.61: 18152 3.61 - 4.26: 28471 4.26 - 4.90: 48837 Nonbonded interactions: 101519 Sorted by model distance: nonbonded pdb=" NE2 GLN A 201 " pdb=" OD1 ASP E 222 " model vdw 1.682 2.520 nonbonded pdb=" OD2 ASP B 67 " pdb=" NH2 ARG B 85 " model vdw 1.886 2.520 nonbonded pdb=" OG SER E 43 " pdb=" OG1 THR E 48 " model vdw 2.062 2.440 nonbonded pdb=" NE2 HIS E 175 " pdb=" OD2 ASP E 222 " model vdw 2.141 2.520 nonbonded pdb=" OE2 GLU A 34 " pdb=" OG1 THR A 36 " model vdw 2.166 2.440 ... (remaining 101514 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 1 through 316 or resid 401 through 402)) selection = chain 'C' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' } ncs_group { reference = (chain 'G' and resid 20 through 127) selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' selection = chain 'K' } 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: 8.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.090 Set scattering table: 0.120 Process input model: 38.610 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.136 12909 Z= 0.437 Angle : 1.165 17.797 17480 Z= 0.632 Chirality : 0.060 0.377 1985 Planarity : 0.012 0.488 2315 Dihedral : 14.131 89.890 4810 Min Nonbonded Distance : 1.682 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 12.70 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.20), residues: 1438 helix: 1.00 (0.25), residues: 329 sheet: 0.78 (0.30), residues: 262 loop : -0.35 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP C 142 HIS 0.013 0.003 HIS D 159 PHE 0.030 0.004 PHE A 250 TYR 0.043 0.003 TYR F 119 ARG 0.014 0.001 ARG F 127 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.317 Fit side-chains REVERT: A 42 CYS cc_start: 0.5936 (m) cc_final: 0.5717 (m) REVERT: B 39 LYS cc_start: 0.7346 (ttmt) cc_final: 0.6690 (ttpt) REVERT: B 167 MET cc_start: 0.6540 (tmm) cc_final: 0.6056 (ttp) REVERT: B 168 GLN cc_start: 0.7363 (mm-40) cc_final: 0.7126 (mm-40) REVERT: C 185 LEU cc_start: 0.7320 (mp) cc_final: 0.7120 (mt) REVERT: C 303 ARG cc_start: 0.7471 (mtp-110) cc_final: 0.7070 (ptm-80) REVERT: D 135 THR cc_start: 0.7938 (t) cc_final: 0.7714 (t) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2672 time to fit residues: 60.3735 Evaluate side-chains 142 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 49 optimal weight: 0.0570 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 1.0902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 ASN C 37 ASN D 159 HIS E 239 ASN F 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.1190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 12909 Z= 0.270 Angle : 0.647 6.916 17480 Z= 0.343 Chirality : 0.044 0.300 1985 Planarity : 0.004 0.080 2315 Dihedral : 5.625 43.066 2117 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.71 % Allowed : 12.30 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.20), residues: 1438 helix: 1.35 (0.26), residues: 339 sheet: 0.55 (0.30), residues: 269 loop : -0.58 (0.19), residues: 830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 142 HIS 0.005 0.001 HIS D 159 PHE 0.015 0.002 PHE A 92 TYR 0.018 0.002 TYR F 119 ARG 0.004 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 185 time to evaluate : 1.201 Fit side-chains REVERT: B 25 ARG cc_start: 0.7839 (ttm170) cc_final: 0.7383 (tpp80) REVERT: B 39 LYS cc_start: 0.7467 (ttmt) cc_final: 0.6785 (ttpt) REVERT: C 27 VAL cc_start: 0.8497 (p) cc_final: 0.8057 (t) REVERT: C 75 ASP cc_start: 0.6667 (m-30) cc_final: 0.6434 (m-30) REVERT: E 171 TRP cc_start: 0.8812 (p90) cc_final: 0.8598 (p90) REVERT: E 232 ASP cc_start: 0.7116 (m-30) cc_final: 0.6873 (m-30) outliers start: 21 outliers final: 17 residues processed: 197 average time/residue: 0.2552 time to fit residues: 71.4787 Evaluate side-chains 174 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 157 time to evaluate : 1.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 40 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 160 optimal weight: 10.0000 chunk 132 optimal weight: 0.7980 chunk 147 optimal weight: 8.9990 chunk 50 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 53 GLN A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 159 HIS E 263 GLN F 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12909 Z= 0.257 Angle : 0.586 6.623 17480 Z= 0.312 Chirality : 0.044 0.296 1985 Planarity : 0.004 0.061 2315 Dihedral : 5.243 42.672 2117 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.01 % Allowed : 13.19 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1438 helix: 1.46 (0.27), residues: 339 sheet: 0.30 (0.30), residues: 281 loop : -0.74 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 142 HIS 0.006 0.001 HIS F 142 PHE 0.017 0.002 PHE C 238 TYR 0.016 0.002 TYR F 119 ARG 0.005 0.000 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 175 time to evaluate : 1.913 Fit side-chains REVERT: A 238 PHE cc_start: 0.7742 (OUTLIER) cc_final: 0.7357 (m-10) REVERT: B 25 ARG cc_start: 0.7818 (ttm170) cc_final: 0.7535 (tpp80) REVERT: B 39 LYS cc_start: 0.7564 (ttmt) cc_final: 0.6876 (ttpt) REVERT: D 115 MET cc_start: 0.8669 (tpt) cc_final: 0.7751 (tpt) REVERT: E 217 GLN cc_start: 0.7144 (tp40) cc_final: 0.6845 (mt0) outliers start: 37 outliers final: 23 residues processed: 197 average time/residue: 0.2485 time to fit residues: 71.2787 Evaluate side-chains 187 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 163 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 113 SER Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 146 optimal weight: 5.9990 chunk 111 optimal weight: 4.9990 chunk 76 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 157 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN C 313 ASN E 53 GLN E 201 GLN F 106 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12909 Z= 0.372 Angle : 0.656 6.741 17480 Z= 0.343 Chirality : 0.045 0.327 1985 Planarity : 0.004 0.056 2315 Dihedral : 5.393 41.454 2117 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.83 % Allowed : 13.11 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.20), residues: 1438 helix: 1.24 (0.27), residues: 333 sheet: -0.22 (0.30), residues: 272 loop : -1.04 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 142 HIS 0.006 0.002 HIS C 175 PHE 0.023 0.002 PHE C 238 TYR 0.015 0.002 TYR F 119 ARG 0.007 0.001 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 172 time to evaluate : 1.280 Fit side-chains revert: symmetry clash REVERT: B 25 ARG cc_start: 0.7838 (ttm170) cc_final: 0.7567 (tpp80) REVERT: B 39 LYS cc_start: 0.7647 (ttmt) cc_final: 0.7107 (mtpt) REVERT: C 27 VAL cc_start: 0.8907 (p) cc_final: 0.8550 (t) REVERT: C 256 MET cc_start: 0.7346 (ttp) cc_final: 0.6938 (tmm) REVERT: D 120 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7398 (mp0) REVERT: E 217 GLN cc_start: 0.7348 (tp40) cc_final: 0.6986 (mt0) outliers start: 47 outliers final: 31 residues processed: 200 average time/residue: 0.2605 time to fit residues: 74.0702 Evaluate side-chains 192 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 160 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 128 GLU Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 131 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 134 optimal weight: 0.6980 chunk 108 optimal weight: 0.0870 chunk 0 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 141 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN E 37 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12909 Z= 0.187 Angle : 0.537 6.281 17480 Z= 0.284 Chirality : 0.042 0.305 1985 Planarity : 0.003 0.052 2315 Dihedral : 5.024 40.410 2117 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.01 % Allowed : 14.33 % Favored : 82.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.20), residues: 1438 helix: 1.50 (0.27), residues: 333 sheet: -0.17 (0.31), residues: 256 loop : -1.04 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.003 0.001 HIS E 7 PHE 0.015 0.001 PHE C 238 TYR 0.017 0.001 TYR F 119 ARG 0.003 0.000 ARG C 291 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 166 time to evaluate : 1.258 Fit side-chains REVERT: A 238 PHE cc_start: 0.7953 (OUTLIER) cc_final: 0.7551 (m-80) REVERT: A 247 ARG cc_start: 0.7998 (mtt180) cc_final: 0.7792 (mtt180) REVERT: B 25 ARG cc_start: 0.7833 (ttm170) cc_final: 0.7585 (tpp80) REVERT: B 39 LYS cc_start: 0.7632 (ttmt) cc_final: 0.7098 (mtpt) REVERT: B 168 GLN cc_start: 0.7278 (mm110) cc_final: 0.6804 (pp30) REVERT: C 27 VAL cc_start: 0.8810 (p) cc_final: 0.8443 (t) REVERT: D 115 MET cc_start: 0.8627 (tpt) cc_final: 0.8323 (mmm) REVERT: E 217 GLN cc_start: 0.7234 (tp40) cc_final: 0.6923 (mt0) outliers start: 37 outliers final: 27 residues processed: 192 average time/residue: 0.2485 time to fit residues: 68.6262 Evaluate side-chains 182 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 202 GLN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 53 optimal weight: 0.5980 chunk 141 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 38 optimal weight: 0.0020 chunk 157 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 73 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN F 47 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12909 Z= 0.205 Angle : 0.538 12.194 17480 Z= 0.281 Chirality : 0.042 0.310 1985 Planarity : 0.003 0.049 2315 Dihedral : 4.879 39.663 2117 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.18 % Allowed : 14.98 % Favored : 81.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.21), residues: 1438 helix: 1.66 (0.27), residues: 329 sheet: -0.18 (0.32), residues: 256 loop : -1.01 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 142 HIS 0.006 0.001 HIS A 7 PHE 0.014 0.001 PHE C 238 TYR 0.024 0.001 TYR A 186 ARG 0.004 0.000 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 167 time to evaluate : 1.345 Fit side-chains REVERT: A 121 ARG cc_start: 0.7878 (ptt180) cc_final: 0.7603 (ptt90) REVERT: A 238 PHE cc_start: 0.7967 (OUTLIER) cc_final: 0.7548 (m-80) REVERT: A 247 ARG cc_start: 0.8043 (mtt180) cc_final: 0.7806 (mtt180) REVERT: B 25 ARG cc_start: 0.7826 (ttm170) cc_final: 0.7585 (tpp80) REVERT: B 39 LYS cc_start: 0.7652 (ttmt) cc_final: 0.7095 (mtpt) REVERT: C 27 VAL cc_start: 0.8836 (p) cc_final: 0.8456 (t) REVERT: C 256 MET cc_start: 0.7278 (ttp) cc_final: 0.6991 (tmm) REVERT: D 115 MET cc_start: 0.8625 (tpt) cc_final: 0.8342 (mmm) REVERT: D 120 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7380 (mp0) REVERT: D 149 MET cc_start: 0.5590 (OUTLIER) cc_final: 0.5122 (ttm) REVERT: E 217 GLN cc_start: 0.7228 (tp40) cc_final: 0.6918 (mt0) REVERT: F 53 ASN cc_start: 0.8940 (t0) cc_final: 0.8447 (t0) outliers start: 39 outliers final: 30 residues processed: 194 average time/residue: 0.2724 time to fit residues: 75.6920 Evaluate side-chains 193 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 160 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 84 SER Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 152 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 88 optimal weight: 0.7980 chunk 157 optimal weight: 6.9990 chunk 98 optimal weight: 0.6980 chunk 95 optimal weight: 1.9990 chunk 72 optimal weight: 0.0010 chunk 97 optimal weight: 0.0170 overall best weight: 0.4224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12909 Z= 0.162 Angle : 0.513 11.508 17480 Z= 0.270 Chirality : 0.041 0.303 1985 Planarity : 0.003 0.047 2315 Dihedral : 4.674 33.335 2117 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.93 % Allowed : 15.64 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.21), residues: 1438 helix: 1.82 (0.27), residues: 329 sheet: -0.09 (0.31), residues: 260 loop : -0.99 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 14 HIS 0.003 0.001 HIS A 7 PHE 0.016 0.001 PHE C 238 TYR 0.021 0.001 TYR A 186 ARG 0.003 0.000 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 172 time to evaluate : 1.447 Fit side-chains REVERT: A 238 PHE cc_start: 0.7875 (OUTLIER) cc_final: 0.7485 (m-80) REVERT: A 247 ARG cc_start: 0.8031 (mtt180) cc_final: 0.7793 (mtt180) REVERT: B 25 ARG cc_start: 0.7810 (ttm170) cc_final: 0.7585 (tpp80) REVERT: B 39 LYS cc_start: 0.7668 (ttmt) cc_final: 0.7102 (mtpt) REVERT: C 27 VAL cc_start: 0.8745 (p) cc_final: 0.8358 (t) REVERT: C 256 MET cc_start: 0.7210 (ttp) cc_final: 0.6939 (tmm) REVERT: D 115 MET cc_start: 0.8607 (tpt) cc_final: 0.8346 (mmm) REVERT: D 120 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7385 (mp0) REVERT: D 149 MET cc_start: 0.5565 (OUTLIER) cc_final: 0.5048 (ttm) REVERT: E 186 TYR cc_start: 0.7915 (m-80) cc_final: 0.7537 (m-80) REVERT: E 217 GLN cc_start: 0.7211 (tp40) cc_final: 0.6884 (mt0) REVERT: F 157 TYR cc_start: 0.6420 (t80) cc_final: 0.5948 (t80) outliers start: 36 outliers final: 27 residues processed: 196 average time/residue: 0.2674 time to fit residues: 74.6836 Evaluate side-chains 191 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 37 ASN Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 149 MET Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 135 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 62 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 123 optimal weight: 2.9990 chunk 142 optimal weight: 10.0000 chunk 150 optimal weight: 9.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 26 HIS ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.3382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 12909 Z= 0.480 Angle : 0.737 12.755 17480 Z= 0.380 Chirality : 0.049 0.360 1985 Planarity : 0.005 0.052 2315 Dihedral : 5.421 36.049 2117 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 16.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.84 % Favored : 94.16 % Rotamer: Outliers : 3.18 % Allowed : 15.88 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.21), residues: 1438 helix: 1.12 (0.28), residues: 333 sheet: -0.85 (0.30), residues: 282 loop : -1.35 (0.19), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 142 HIS 0.007 0.002 HIS A 7 PHE 0.031 0.003 PHE C 238 TYR 0.017 0.003 TYR C 186 ARG 0.008 0.001 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 173 time to evaluate : 1.400 Fit side-chains revert: symmetry clash REVERT: B 25 ARG cc_start: 0.7893 (ttm170) cc_final: 0.7590 (tpp80) REVERT: B 39 LYS cc_start: 0.7699 (ttmt) cc_final: 0.7143 (mtpt) REVERT: D 115 MET cc_start: 0.8640 (tpt) cc_final: 0.7801 (tpt) REVERT: D 120 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: E 37 ASN cc_start: 0.8590 (p0) cc_final: 0.8355 (p0) REVERT: E 186 TYR cc_start: 0.8336 (m-80) cc_final: 0.8055 (m-10) REVERT: E 217 GLN cc_start: 0.7381 (tp40) cc_final: 0.7099 (mt0) REVERT: E 271 ASP cc_start: 0.7786 (p0) cc_final: 0.7366 (t0) outliers start: 39 outliers final: 30 residues processed: 202 average time/residue: 0.2903 time to fit residues: 83.0844 Evaluate side-chains 191 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 21 GLU Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 2.9990 chunk 146 optimal weight: 5.9990 chunk 150 optimal weight: 8.9990 chunk 88 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 132 optimal weight: 0.9980 chunk 138 optimal weight: 0.7980 chunk 145 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN F 26 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12909 Z= 0.220 Angle : 0.568 12.820 17480 Z= 0.297 Chirality : 0.043 0.319 1985 Planarity : 0.003 0.048 2315 Dihedral : 4.999 35.551 2117 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.61 % Allowed : 16.45 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.74 (0.21), residues: 1438 helix: 1.52 (0.28), residues: 329 sheet: -0.75 (0.30), residues: 276 loop : -1.26 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 142 HIS 0.006 0.001 HIS A 7 PHE 0.017 0.001 PHE C 238 TYR 0.021 0.002 TYR C 186 ARG 0.008 0.000 ARG F 25 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 178 time to evaluate : 1.448 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8018 (OUTLIER) cc_final: 0.7568 (m-80) REVERT: B 25 ARG cc_start: 0.7841 (ttm170) cc_final: 0.7585 (tpp80) REVERT: B 39 LYS cc_start: 0.7674 (ttmt) cc_final: 0.7134 (mtpt) REVERT: C 27 VAL cc_start: 0.8867 (p) cc_final: 0.8531 (t) REVERT: D 115 MET cc_start: 0.8604 (tpt) cc_final: 0.7885 (tpt) REVERT: D 120 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: E 37 ASN cc_start: 0.8498 (p0) cc_final: 0.8271 (p0) REVERT: E 186 TYR cc_start: 0.8075 (m-80) cc_final: 0.7704 (m-80) REVERT: E 217 GLN cc_start: 0.7323 (tp40) cc_final: 0.7020 (mt0) REVERT: F 26 HIS cc_start: 0.6346 (OUTLIER) cc_final: 0.5932 (m90) REVERT: F 157 TYR cc_start: 0.6485 (t80) cc_final: 0.6012 (t80) outliers start: 32 outliers final: 28 residues processed: 202 average time/residue: 0.2661 time to fit residues: 76.8987 Evaluate side-chains 202 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 171 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 12 ASN Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 154 optimal weight: 10.0000 chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 162 optimal weight: 5.9990 chunk 149 optimal weight: 9.9990 chunk 129 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 123 ASN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12909 Z= 0.264 Angle : 0.579 12.679 17480 Z= 0.303 Chirality : 0.044 0.328 1985 Planarity : 0.003 0.049 2315 Dihedral : 4.935 35.061 2117 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.69 % Allowed : 17.26 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.21), residues: 1438 helix: 1.52 (0.28), residues: 329 sheet: -0.77 (0.31), residues: 276 loop : -1.28 (0.19), residues: 833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 142 HIS 0.009 0.001 HIS F 26 PHE 0.020 0.002 PHE C 238 TYR 0.018 0.002 TYR C 186 ARG 0.006 0.000 ARG E 47 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2876 Ramachandran restraints generated. 1438 Oldfield, 0 Emsley, 1438 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 175 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.8029 (OUTLIER) cc_final: 0.7562 (m-80) REVERT: A 256 MET cc_start: 0.8144 (ptm) cc_final: 0.7892 (ttp) REVERT: B 25 ARG cc_start: 0.7857 (ttm170) cc_final: 0.7593 (tpp80) REVERT: B 39 LYS cc_start: 0.7678 (ttmt) cc_final: 0.7127 (mtpt) REVERT: C 27 VAL cc_start: 0.8890 (p) cc_final: 0.8558 (t) REVERT: D 115 MET cc_start: 0.8610 (tpt) cc_final: 0.7888 (tpt) REVERT: D 120 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7381 (mp0) REVERT: E 37 ASN cc_start: 0.8458 (p0) cc_final: 0.8204 (p0) REVERT: E 186 TYR cc_start: 0.8101 (m-80) cc_final: 0.7751 (m-80) REVERT: E 217 GLN cc_start: 0.7320 (tp40) cc_final: 0.7027 (mt0) REVERT: F 157 TYR cc_start: 0.6456 (t80) cc_final: 0.6017 (t80) outliers start: 33 outliers final: 27 residues processed: 201 average time/residue: 0.2673 time to fit residues: 76.0301 Evaluate side-chains 202 residues out of total 1228 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 238 PHE Chi-restraints excluded: chain B residue 43 SER Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 67 ASP Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 151 SER Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 311 MET Chi-restraints excluded: chain D residue 55 LEU Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 128 SER Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain E residue 307 LEU Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 137 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 119 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 129 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 132 optimal weight: 0.9980 chunk 16 optimal weight: 0.0770 chunk 23 optimal weight: 0.8980 chunk 113 optimal weight: 7.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 182 GLN ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 313 ASN ** C 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 26 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.170321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.150925 restraints weight = 16365.650| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.14 r_work: 0.3642 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12909 Z= 0.273 Angle : 0.579 12.607 17480 Z= 0.303 Chirality : 0.044 0.336 1985 Planarity : 0.004 0.052 2315 Dihedral : 4.884 34.387 2117 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.77 % Allowed : 17.10 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.21), residues: 1438 helix: 1.68 (0.28), residues: 323 sheet: -0.79 (0.31), residues: 276 loop : -1.31 (0.19), residues: 839 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP C 142 HIS 0.014 0.001 HIS F 26 PHE 0.018 0.002 PHE C 238 TYR 0.017 0.002 TYR C 186 ARG 0.010 0.001 ARG A 121 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2783.17 seconds wall clock time: 50 minutes 49.86 seconds (3049.86 seconds total)