Starting phenix.real_space_refine on Sat Jan 18 18:59:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ut9_42534/01_2025/8ut9_42534.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ut9_42534/01_2025/8ut9_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/cci-nas-00/data/ceres_data/8ut9_42534/01_2025/8ut9_42534.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ut9_42534/01_2025/8ut9_42534.map" model { file = "/net/cci-nas-00/data/ceres_data/8ut9_42534/01_2025/8ut9_42534.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ut9_42534/01_2025/8ut9_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. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/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: 7.51, per 1000 atoms: 0.59 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=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: 2.95 Conformation dependent library (CDL) restraints added in 1.4 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: 4.33 Time building geometry restraints manager: 3.45 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: 0.00 - 3.56: 17126 3.56 - 7.12: 328 7.12 - 10.68: 22 10.68 - 14.24: 3 14.24 - 17.80: 1 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 3.120 nonbonded pdb=" OD2 ASP B 67 " pdb=" NH2 ARG B 85 " model vdw 1.886 3.120 nonbonded pdb=" OG SER E 43 " pdb=" OG1 THR E 48 " model vdw 2.062 3.040 nonbonded pdb=" NE2 HIS E 175 " pdb=" OD2 ASP E 222 " model vdw 2.141 3.120 nonbonded pdb=" OE2 GLU A 34 " pdb=" OG1 THR A 36 " model vdw 2.166 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 12.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 30.730 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.270 ------------------------------------------------------------------------------- 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 to be fit. 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: 0.2799 time to fit residues: 63.0851 Evaluate side-chains 142 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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: 0.8980 chunk 123 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 127 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 60 ASN C 239 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 159 HIS E 239 ASN F 106 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.181285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.160557 restraints weight = 16103.268| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.34 r_work: 0.3736 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 12909 Z= 0.234 Angle : 0.645 6.918 17480 Z= 0.343 Chirality : 0.044 0.300 1985 Planarity : 0.004 0.081 2315 Dihedral : 5.488 43.061 2117 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.22 % Allowed : 12.54 % Favored : 86.24 % 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: 0.21 (0.20), residues: 1438 helix: 1.39 (0.26), residues: 336 sheet: 0.60 (0.30), residues: 271 loop : -0.53 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 142 HIS 0.008 0.001 HIS B 142 PHE 0.015 0.002 PHE C 92 TYR 0.017 0.001 TYR F 119 ARG 0.004 0.001 ARG F 25 *********************** 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 208 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 193 time to evaluate : 1.643 Fit side-chains revert: symmetry clash REVERT: A 232 ASP cc_start: 0.7549 (t0) cc_final: 0.7132 (t0) REVERT: A 247 ARG cc_start: 0.7769 (mtt180) cc_final: 0.7509 (mtt180) REVERT: B 25 ARG cc_start: 0.7891 (ttm170) cc_final: 0.7400 (tpp80) REVERT: B 39 LYS cc_start: 0.7355 (ttmt) cc_final: 0.6635 (ttpt) REVERT: E 232 ASP cc_start: 0.7003 (m-30) cc_final: 0.6769 (m-30) outliers start: 15 outliers final: 11 residues processed: 202 average time/residue: 0.2723 time to fit residues: 78.4040 Evaluate side-chains 168 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain C residue 194 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 144 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 130 optimal weight: 0.9990 chunk 113 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 152 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 124 optimal weight: 0.0770 overall best weight: 0.8544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 HIS A 123 ASN A 287 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 GLN D 61 GLN D 159 HIS E 239 ASN F 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.180158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.159475 restraints weight = 16418.151| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 2.34 r_work: 0.3728 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12909 Z= 0.226 Angle : 0.575 6.453 17480 Z= 0.306 Chirality : 0.043 0.284 1985 Planarity : 0.004 0.060 2315 Dihedral : 5.104 39.930 2117 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.12 % Allowed : 13.68 % Favored : 84.20 % 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: 0.08 (0.21), residues: 1438 helix: 1.43 (0.26), residues: 339 sheet: 0.43 (0.30), residues: 281 loop : -0.67 (0.20), residues: 818 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 14 HIS 0.004 0.001 HIS D 159 PHE 0.017 0.002 PHE C 238 TYR 0.012 0.001 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 203 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.265 Fit side-chains revert: symmetry clash REVERT: A 121 ARG cc_start: 0.7768 (ptt180) cc_final: 0.7539 (ptt90) REVERT: A 238 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.7147 (m-10) REVERT: A 247 ARG cc_start: 0.7965 (mtt180) cc_final: 0.7722 (mtt180) REVERT: B 39 LYS cc_start: 0.7477 (ttmt) cc_final: 0.6752 (ttpt) REVERT: B 168 GLN cc_start: 0.7351 (mm110) cc_final: 0.6887 (pp30) REVERT: D 115 MET cc_start: 0.8704 (tpt) cc_final: 0.7752 (tpt) outliers start: 26 outliers final: 15 residues processed: 194 average time/residue: 0.2781 time to fit residues: 76.2830 Evaluate side-chains 181 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.318 ------------------------------------------------------------------------------- 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 110 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 194 THR Chi-restraints excluded: chain C residue 222 ASP Chi-restraints excluded: chain C residue 225 TRP Chi-restraints excluded: chain D residue 55 LEU 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 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 10 optimal weight: 1.9990 chunk 132 optimal weight: 0.2980 chunk 123 optimal weight: 1.9990 chunk 145 optimal weight: 10.0000 chunk 140 optimal weight: 0.0070 chunk 119 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 154 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.0402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN A 217 GLN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN E 53 GLN E 239 ASN E 263 GLN F 106 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.175400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.154661 restraints weight = 16482.492| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.34 r_work: 0.3695 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7701 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12909 Z= 0.253 Angle : 0.573 6.327 17480 Z= 0.304 Chirality : 0.043 0.295 1985 Planarity : 0.004 0.054 2315 Dihedral : 5.008 38.938 2117 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.93 % Allowed : 13.03 % Favored : 84.04 % 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: -0.14 (0.20), residues: 1438 helix: 1.52 (0.27), residues: 333 sheet: 0.20 (0.30), residues: 270 loop : -0.88 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 142 HIS 0.004 0.001 HIS F 159 PHE 0.014 0.002 PHE C 136 TYR 0.011 0.001 TYR F 119 ARG 0.005 0.000 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 213 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.246 Fit side-chains revert: symmetry clash REVERT: A 238 PHE cc_start: 0.7915 (OUTLIER) cc_final: 0.7426 (m-10) REVERT: A 247 ARG cc_start: 0.8263 (mtt180) cc_final: 0.7951 (mtt180) REVERT: B 25 ARG cc_start: 0.8148 (ttm170) cc_final: 0.7911 (tpp80) REVERT: B 39 LYS cc_start: 0.7621 (ttmt) cc_final: 0.6884 (ttpt) REVERT: B 168 GLN cc_start: 0.7362 (mm110) cc_final: 0.6776 (pp30) REVERT: C 256 MET cc_start: 0.7454 (ttp) cc_final: 0.7220 (tmm) REVERT: D 115 MET cc_start: 0.8718 (tpt) cc_final: 0.8363 (mmm) REVERT: E 217 GLN cc_start: 0.7176 (tp40) cc_final: 0.6840 (mt0) outliers start: 36 outliers final: 23 residues processed: 203 average time/residue: 0.2773 time to fit residues: 79.4051 Evaluate side-chains 187 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASN Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 217 GLN 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 C residue 130 ARG Chi-restraints excluded: chain C residue 160 LYS Chi-restraints excluded: chain C residue 194 THR 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 75 LYS Chi-restraints excluded: chain D residue 102 MET 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 256 MET Chi-restraints excluded: chain E residue 272 CYS Chi-restraints excluded: chain F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 17 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 122 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 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 313 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 61 GLN E 201 GLN F 47 GLN F 106 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.171478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.150659 restraints weight = 16728.519| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.31 r_work: 0.3633 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3498 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 12909 Z= 0.374 Angle : 0.638 6.993 17480 Z= 0.335 Chirality : 0.045 0.321 1985 Planarity : 0.004 0.052 2315 Dihedral : 5.187 37.780 2117 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.66 % Allowed : 13.93 % Favored : 82.41 % 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: -0.49 (0.20), residues: 1438 helix: 1.25 (0.27), residues: 333 sheet: -0.10 (0.31), residues: 270 loop : -1.08 (0.19), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 142 HIS 0.006 0.002 HIS E 8 PHE 0.024 0.002 PHE C 238 TYR 0.013 0.002 TYR D 119 ARG 0.008 0.001 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 228 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 121 ARG cc_start: 0.8125 (ptt90) cc_final: 0.7799 (ptt-90) REVERT: A 222 ASP cc_start: 0.8433 (m-30) cc_final: 0.8136 (m-30) REVERT: A 238 PHE cc_start: 0.8152 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: A 247 ARG cc_start: 0.8452 (mtt180) cc_final: 0.8055 (mtt180) REVERT: B 25 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7925 (tpp80) REVERT: B 39 LYS cc_start: 0.7687 (ttmt) cc_final: 0.6979 (ttpt) REVERT: C 37 ASN cc_start: 0.8537 (OUTLIER) cc_final: 0.8189 (p0) REVERT: D 120 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7729 (mp0) REVERT: D 125 GLN cc_start: 0.7277 (tt0) cc_final: 0.7046 (tt0) REVERT: D 163 ARG cc_start: 0.6358 (mmt90) cc_final: 0.6095 (mtm180) REVERT: E 217 GLN cc_start: 0.7389 (tp40) cc_final: 0.6902 (mt0) REVERT: E 265 ASP cc_start: 0.7598 (t0) cc_final: 0.7384 (t70) REVERT: E 271 ASP cc_start: 0.8093 (p0) cc_final: 0.7346 (t0) outliers start: 45 outliers final: 30 residues processed: 213 average time/residue: 0.2764 time to fit residues: 82.7257 Evaluate side-chains 200 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 167 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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 12 ASN Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 217 GLN 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 C residue 27 VAL Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 37 ASN 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 225 TRP Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 278 THR Chi-restraints excluded: chain C residue 304 SER 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 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 F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 115 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 81 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 142 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 135 optimal weight: 0.7980 chunk 125 optimal weight: 0.4980 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 123 ASN C 313 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN E 239 ASN ** E 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN ** F 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.151693 restraints weight = 16704.486| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.37 r_work: 0.3658 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12909 Z= 0.221 Angle : 0.561 11.679 17480 Z= 0.294 Chirality : 0.042 0.305 1985 Planarity : 0.003 0.050 2315 Dihedral : 5.000 37.353 2117 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 2.44 % Allowed : 15.88 % Favored : 81.68 % 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: -0.45 (0.20), residues: 1438 helix: 1.41 (0.27), residues: 333 sheet: -0.10 (0.32), residues: 256 loop : -1.09 (0.19), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 142 HIS 0.004 0.001 HIS D 142 PHE 0.021 0.002 PHE C 238 TYR 0.022 0.002 TYR A 186 ARG 0.004 0.000 ARG E 22 *********************** 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 215 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 185 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8446 (m-30) cc_final: 0.8225 (m-30) REVERT: A 238 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: A 247 ARG cc_start: 0.8413 (mtt180) cc_final: 0.8074 (mtt180) REVERT: B 25 ARG cc_start: 0.8164 (ttm170) cc_final: 0.7921 (tpp80) REVERT: B 39 LYS cc_start: 0.7670 (ttmt) cc_final: 0.6961 (ttpt) REVERT: B 168 GLN cc_start: 0.7439 (mm110) cc_final: 0.6837 (pp30) REVERT: C 256 MET cc_start: 0.7572 (ttp) cc_final: 0.7253 (tmm) REVERT: D 115 MET cc_start: 0.8690 (tpt) cc_final: 0.8447 (mmm) REVERT: D 120 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: D 163 ARG cc_start: 0.6355 (mmt90) cc_final: 0.6107 (mtm180) REVERT: E 217 GLN cc_start: 0.7276 (tp40) cc_final: 0.6853 (mt0) REVERT: F 53 ASN cc_start: 0.8996 (t0) cc_final: 0.8527 (t0) outliers start: 30 outliers final: 22 residues processed: 206 average time/residue: 0.2683 time to fit residues: 78.8154 Evaluate side-chains 194 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 1.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 3 ILE Chi-restraints excluded: chain A residue 12 ASN 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 56 ILE Chi-restraints excluded: chain B residue 110 LEU 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 194 THR 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 75 LYS Chi-restraints excluded: chain D residue 102 MET Chi-restraints excluded: chain D residue 120 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 27 optimal weight: 0.0030 chunk 9 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** A 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.170862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.150604 restraints weight = 16576.300| |-----------------------------------------------------------------------------| r_work (start): 0.3752 rms_B_bonded: 2.25 r_work: 0.3649 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3515 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12909 Z= 0.292 Angle : 0.585 10.906 17480 Z= 0.306 Chirality : 0.044 0.318 1985 Planarity : 0.003 0.049 2315 Dihedral : 4.969 34.063 2117 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 3.09 % Allowed : 15.72 % Favored : 81.19 % 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: -0.55 (0.21), residues: 1438 helix: 1.36 (0.27), residues: 333 sheet: -0.26 (0.32), residues: 258 loop : -1.13 (0.19), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP C 142 HIS 0.004 0.001 HIS E 8 PHE 0.025 0.002 PHE C 238 TYR 0.014 0.002 TYR A 186 ARG 0.006 0.001 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 207 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8458 (m-30) cc_final: 0.8205 (m-30) REVERT: A 238 PHE cc_start: 0.8174 (OUTLIER) cc_final: 0.7784 (m-80) REVERT: A 247 ARG cc_start: 0.8482 (mtt180) cc_final: 0.8141 (mtt180) REVERT: B 25 ARG cc_start: 0.8118 (ttm170) cc_final: 0.7873 (tpp80) REVERT: B 39 LYS cc_start: 0.7691 (ttmt) cc_final: 0.6978 (ttpt) REVERT: C 256 MET cc_start: 0.7569 (ttp) cc_final: 0.7206 (tmm) REVERT: D 115 MET cc_start: 0.8698 (tpt) cc_final: 0.8459 (mmm) REVERT: D 120 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7694 (mp0) REVERT: D 125 GLN cc_start: 0.7284 (OUTLIER) cc_final: 0.7074 (tt0) REVERT: E 217 GLN cc_start: 0.7287 (tp40) cc_final: 0.6872 (mt0) REVERT: E 271 ASP cc_start: 0.8019 (p0) cc_final: 0.7277 (t0) outliers start: 38 outliers final: 30 residues processed: 198 average time/residue: 0.2798 time to fit residues: 76.9161 Evaluate side-chains 197 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.258 ------------------------------------------------------------------------------- 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 12 ASN 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 A residue 260 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 160 LYS Chi-restraints excluded: chain C residue 162 THR Chi-restraints excluded: chain C residue 194 THR 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 304 SER 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 125 GLN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 61 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 F residue 26 HIS Chi-restraints excluded: chain F residue 110 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 84 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 63 optimal weight: 0.3980 chunk 138 optimal weight: 2.9990 chunk 109 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 131 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN B 26 HIS C 37 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.172435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.152252 restraints weight = 16594.265| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.26 r_work: 0.3668 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12909 Z= 0.220 Angle : 0.545 10.876 17480 Z= 0.286 Chirality : 0.042 0.307 1985 Planarity : 0.003 0.049 2315 Dihedral : 4.906 42.079 2117 Min Nonbonded Distance : 2.305 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.77 % Allowed : 16.37 % Favored : 80.86 % 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: -0.47 (0.21), residues: 1438 helix: 1.49 (0.27), residues: 333 sheet: -0.19 (0.32), residues: 252 loop : -1.12 (0.19), residues: 853 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP C 142 HIS 0.003 0.001 HIS E 7 PHE 0.022 0.001 PHE C 238 TYR 0.013 0.001 TYR A 186 ARG 0.008 0.000 ARG E 47 *********************** 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 208 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 1.242 Fit side-chains revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8403 (m-30) cc_final: 0.8183 (m-30) REVERT: A 238 PHE cc_start: 0.8145 (OUTLIER) cc_final: 0.7752 (m-80) REVERT: A 247 ARG cc_start: 0.8500 (mtt180) cc_final: 0.8176 (mtt180) REVERT: B 25 ARG cc_start: 0.8114 (ttm170) cc_final: 0.7879 (tpp80) REVERT: B 39 LYS cc_start: 0.7691 (ttmt) cc_final: 0.6981 (ttpt) REVERT: B 168 GLN cc_start: 0.7506 (mm-40) cc_final: 0.6905 (pp30) REVERT: C 256 MET cc_start: 0.7497 (ttp) cc_final: 0.7141 (tmm) REVERT: D 115 MET cc_start: 0.8666 (tpt) cc_final: 0.8459 (mmm) REVERT: D 120 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7686 (mp0) REVERT: E 217 GLN cc_start: 0.7245 (tp40) cc_final: 0.6845 (mt0) REVERT: F 53 ASN cc_start: 0.8999 (t0) cc_final: 0.8521 (t0) REVERT: F 157 TYR cc_start: 0.6560 (t80) cc_final: 0.6090 (t80) outliers start: 34 outliers final: 26 residues processed: 198 average time/residue: 0.2668 time to fit residues: 75.0354 Evaluate side-chains 199 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 171 time to evaluate : 1.298 ------------------------------------------------------------------------------- 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 12 ASN 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 A residue 260 SER Chi-restraints excluded: chain B residue 56 ILE 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 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 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 61 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 163 random chunks: chunk 78 optimal weight: 0.6980 chunk 53 optimal weight: 0.3980 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN C 229 ASN C 313 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 12 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.168763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.147606 restraints weight = 16637.273| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.38 r_work: 0.3604 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3464 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 12909 Z= 0.343 Angle : 0.616 11.086 17480 Z= 0.324 Chirality : 0.045 0.331 1985 Planarity : 0.004 0.049 2315 Dihedral : 5.085 42.858 2117 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 2.93 % Allowed : 16.37 % Favored : 80.70 % 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: 1.31 (0.27), residues: 333 sheet: -0.50 (0.32), residues: 264 loop : -1.29 (0.19), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 142 HIS 0.005 0.001 HIS E 8 PHE 0.026 0.002 PHE C 238 TYR 0.016 0.002 TYR C 186 ARG 0.006 0.001 ARG E 47 *********************** 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 215 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 179 time to evaluate : 1.512 Fit side-chains revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8487 (m-30) cc_final: 0.8209 (m-30) REVERT: A 238 PHE cc_start: 0.8233 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: A 247 ARG cc_start: 0.8564 (mtt180) cc_final: 0.8217 (mtt180) REVERT: B 25 ARG cc_start: 0.8133 (ttm170) cc_final: 0.7858 (tpp80) REVERT: B 39 LYS cc_start: 0.7701 (ttmt) cc_final: 0.6994 (ttpt) REVERT: C 256 MET cc_start: 0.7610 (ttp) cc_final: 0.7152 (tmm) REVERT: D 19 ASP cc_start: 0.7972 (p0) cc_final: 0.7676 (p0) REVERT: D 115 MET cc_start: 0.8710 (tpt) cc_final: 0.8481 (mmm) REVERT: D 120 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: D 125 GLN cc_start: 0.7316 (OUTLIER) cc_final: 0.7108 (tt0) REVERT: E 217 GLN cc_start: 0.7400 (tp40) cc_final: 0.6929 (mt0) REVERT: F 53 ASN cc_start: 0.9018 (t0) cc_final: 0.8522 (t0) REVERT: F 157 TYR cc_start: 0.6594 (t80) cc_final: 0.6133 (t80) outliers start: 36 outliers final: 29 residues processed: 204 average time/residue: 0.2615 time to fit residues: 76.6296 Evaluate side-chains 201 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 169 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 12 ASN 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 A residue 260 SER 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 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 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain D residue 125 GLN Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 61 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 133 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 130 optimal weight: 0.9990 chunk 79 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 36 optimal weight: 0.0060 chunk 45 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 159 optimal weight: 10.0000 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.172236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.151307 restraints weight = 16562.088| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.38 r_work: 0.3640 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12909 Z= 0.197 Angle : 0.552 10.466 17480 Z= 0.291 Chirality : 0.042 0.308 1985 Planarity : 0.003 0.047 2315 Dihedral : 4.890 33.145 2117 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.28 % Allowed : 17.67 % 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: -0.56 (0.21), residues: 1438 helix: 1.70 (0.27), residues: 323 sheet: -0.31 (0.32), residues: 254 loop : -1.26 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 142 HIS 0.004 0.001 HIS E 7 PHE 0.021 0.001 PHE C 238 TYR 0.017 0.001 TYR C 186 ARG 0.007 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 201 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.348 Fit side-chains revert: symmetry clash REVERT: A 222 ASP cc_start: 0.8458 (m-30) cc_final: 0.8207 (m-30) REVERT: A 238 PHE cc_start: 0.8137 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: A 247 ARG cc_start: 0.8492 (mtt180) cc_final: 0.8175 (mtt180) REVERT: B 25 ARG cc_start: 0.8089 (ttm170) cc_final: 0.7865 (tpp80) REVERT: B 39 LYS cc_start: 0.7660 (ttmt) cc_final: 0.6956 (ttpt) REVERT: B 168 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6889 (pp30) REVERT: C 256 MET cc_start: 0.7548 (ttp) cc_final: 0.7160 (tmm) REVERT: D 19 ASP cc_start: 0.7984 (p0) cc_final: 0.7715 (p0) REVERT: D 37 ASP cc_start: 0.7808 (t0) cc_final: 0.7521 (t0) REVERT: D 120 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7662 (mp0) REVERT: E 217 GLN cc_start: 0.7311 (tp40) cc_final: 0.6846 (mt0) REVERT: F 157 TYR cc_start: 0.6642 (t80) cc_final: 0.6203 (t80) outliers start: 28 outliers final: 22 residues processed: 194 average time/residue: 0.2666 time to fit residues: 73.6897 Evaluate side-chains 195 residues out of total 1228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 171 time to evaluate : 1.521 ------------------------------------------------------------------------------- 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 12 ASN 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 36 THR Chi-restraints excluded: chain C residue 130 ARG 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 102 MET Chi-restraints excluded: chain D residue 120 GLU Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain E residue 37 ASN Chi-restraints excluded: chain E residue 66 CYS Chi-restraints excluded: chain E residue 272 CYS 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 143 optimal weight: 7.9990 chunk 67 optimal weight: 0.0370 chunk 46 optimal weight: 0.3980 chunk 101 optimal weight: 3.9990 chunk 159 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 overall best weight: 1.8662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN ** D 26 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 ASN F 12 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.171570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.150668 restraints weight = 16571.774| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.38 r_work: 0.3637 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 12909 Z= 0.279 Angle : 0.802 59.174 17480 Z= 0.469 Chirality : 0.049 1.046 1985 Planarity : 0.003 0.047 2315 Dihedral : 4.929 33.118 2117 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.44 % Allowed : 17.43 % Favored : 80.13 % Cbeta Deviations : 0.06 % 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: -0.57 (0.21), residues: 1438 helix: 1.67 (0.27), residues: 323 sheet: -0.31 (0.32), residues: 254 loop : -1.26 (0.19), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 142 HIS 0.004 0.001 HIS E 7 PHE 0.028 0.002 PHE C 242 TYR 0.014 0.001 TYR C 186 ARG 0.006 0.000 ARG E 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5764.23 seconds wall clock time: 105 minutes 8.63 seconds (6308.63 seconds total)