Starting phenix.real_space_refine on Wed Apr 17 16:59:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/04_2024/6gen_4396_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/04_2024/6gen_4396.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/04_2024/6gen_4396.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/04_2024/6gen_4396.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/04_2024/6gen_4396_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6gen_4396/04_2024/6gen_4396_updated.pdb" } resolution = 3.6 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= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 966 atoms to isotropic. 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: 9 Type Number sf(0) Gaussians Zn 2 6.06 5 P 362 5.49 5 Mg 8 5.21 5 S 118 5.16 5 Be 2 3.05 5 C 26898 2.51 5 N 7881 2.21 5 O 9204 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 36": "NH1" <-> "NH2" Residue "C ARG 45": "NH1" <-> "NH2" Residue "C ARG 95": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ARG 45": "NH1" <-> "NH2" Residue "D ARG 95": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 36": "NH1" <-> "NH2" Residue "E TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 72": "NH1" <-> "NH2" Residue "E ARG 82": "NH1" <-> "NH2" Residue "E ARG 89": "NH1" <-> "NH2" Residue "F ARG 30": "NH1" <-> "NH2" Residue "F ARG 36": "NH1" <-> "NH2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 72": "NH1" <-> "NH2" Residue "F ARG 82": "NH1" <-> "NH2" Residue "F ARG 89": "NH1" <-> "NH2" Residue "G ARG 95": "NH1" <-> "NH2" Residue "H ARG 95": "NH1" <-> "NH2" Residue "M ARG 693": "NH1" <-> "NH2" Residue "M ARG 697": "NH1" <-> "NH2" Residue "M TYR 699": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 766": "NH1" <-> "NH2" Residue "M PHE 767": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 787": "NH1" <-> "NH2" Residue "M ARG 815": "NH1" <-> "NH2" Residue "M ARG 833": "NH1" <-> "NH2" Residue "M ARG 926": "NH1" <-> "NH2" Residue "M ARG 956": "NH1" <-> "NH2" Residue "M ARG 967": "NH1" <-> "NH2" Residue "M PHE 999": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 1018": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1023": "NH1" <-> "NH2" Residue "M ARG 1133": "NH1" <-> "NH2" Residue "M ASP 1159": "OD1" <-> "OD2" Residue "M ARG 1291": "NH1" <-> "NH2" Residue "M ARG 1313": "NH1" <-> "NH2" Residue "M ARG 1357": "NH1" <-> "NH2" Residue "M PHE 1369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 1387": "NH1" <-> "NH2" Residue "R PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 59": "NH1" <-> "NH2" Residue "R PHE 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 221": "NH1" <-> "NH2" Residue "R ARG 234": "NH1" <-> "NH2" Residue "R PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 286": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 288": "NH1" <-> "NH2" Residue "R ARG 291": "NH1" <-> "NH2" Residue "R PHE 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 434": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 179": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 276": "NH1" <-> "NH2" Residue "T ARG 23": "NH1" <-> "NH2" Residue "T GLU 37": "OE1" <-> "OE2" Residue "T TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T ARG 191": "NH1" <-> "NH2" Residue "T ARG 258": "NH1" <-> "NH2" Residue "T ARG 348": "NH1" <-> "NH2" Residue "T ARG 392": "NH1" <-> "NH2" Residue "T ARG 413": "NH1" <-> "NH2" Residue "T GLU 441": "OE1" <-> "OE2" Residue "T TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 52": "NH1" <-> "NH2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "U ARG 122": "NH1" <-> "NH2" Residue "U TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "U PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 266": "NH1" <-> "NH2" Residue "U ARG 311": "NH1" <-> "NH2" Residue "U ARG 333": "NH1" <-> "NH2" Residue "U ASP 349": "OD1" <-> "OD2" Residue "U ARG 397": "NH1" <-> "NH2" Residue "U ARG 413": "NH1" <-> "NH2" Residue "U GLU 421": "OE1" <-> "OE2" Residue "U ARG 425": "NH1" <-> "NH2" Residue "U ARG 435": "NH1" <-> "NH2" Residue "U TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 23": "NH1" <-> "NH2" Residue "V GLU 37": "OE1" <-> "OE2" Residue "V ARG 191": "NH1" <-> "NH2" Residue "V ARG 258": "NH1" <-> "NH2" Residue "V ARG 348": "NH1" <-> "NH2" Residue "V ARG 392": "NH1" <-> "NH2" Residue "V ARG 413": "NH1" <-> "NH2" Residue "V GLU 441": "OE1" <-> "OE2" Residue "V TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 52": "NH1" <-> "NH2" Residue "W ARG 69": "NH1" <-> "NH2" Residue "W ARG 122": "NH1" <-> "NH2" Residue "W TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "W PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 266": "NH1" <-> "NH2" Residue "W ARG 311": "NH1" <-> "NH2" Residue "W ARG 333": "NH1" <-> "NH2" Residue "W ASP 349": "OD1" <-> "OD2" Residue "W ARG 397": "NH1" <-> "NH2" Residue "W ARG 413": "NH1" <-> "NH2" Residue "W GLU 421": "OE1" <-> "OE2" Residue "W ARG 425": "NH1" <-> "NH2" Residue "W ARG 435": "NH1" <-> "NH2" Residue "W TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X GLU 37": "OE1" <-> "OE2" Residue "X TYR 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 191": "NH1" <-> "NH2" Residue "X ARG 258": "NH1" <-> "NH2" Residue "X ARG 348": "NH1" <-> "NH2" Residue "X ARG 392": "NH1" <-> "NH2" Residue "X ARG 413": "NH1" <-> "NH2" Residue "X GLU 441": "OE1" <-> "OE2" Residue "X TYR 462": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Y ARG 69": "NH1" <-> "NH2" Residue "Y ARG 122": "NH1" <-> "NH2" Residue "Y TYR 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 204": "NH1" <-> "NH2" Residue "Y PHE 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y PHE 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 266": "NH1" <-> "NH2" Residue "Y ARG 311": "NH1" <-> "NH2" Residue "Y ARG 333": "NH1" <-> "NH2" Residue "Y ASP 349": "OD1" <-> "OD2" Residue "Y ARG 397": "NH1" <-> "NH2" Residue "Y ARG 413": "NH1" <-> "NH2" Residue "Y GLU 421": "OE1" <-> "OE2" Residue "Y ARG 425": "NH1" <-> "NH2" Residue "Y ARG 435": "NH1" <-> "NH2" Residue "Y TYR 447": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 44481 Number of models: 1 Model: "" Number of chains: 29 Chain: "Z" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 655 Classifications: {'peptide': 131} Incomplete info: {'truncation_to_alanine': 131} Link IDs: {'TRANS': 130} Unresolved non-hydrogen bonds: 262 Unresolved non-hydrogen angles: 393 Unresolved non-hydrogen dihedrals: 131 Planarities with less than four sites: {'UNK:plan-1': 131} Unresolved non-hydrogen planarities: 131 Chain: "A" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 796 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 651 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "F" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 779 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "G" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 746 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "H" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 712 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "I" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 3525 Classifications: {'DNA': 173} Link IDs: {'rna3p': 172} Chain: "J" Number of atoms: 3568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 3568 Classifications: {'DNA': 173} Link IDs: {'rna3p': 172} Chain: "M" Number of atoms: 5398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 688, 5398 Classifications: {'peptide': 688} Incomplete info: {'truncation_to_alanine': 57} Link IDs: {'PTRANS': 19, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 241 Unresolved non-hydrogen angles: 296 Unresolved non-hydrogen dihedrals: 206 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 7, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 4, 'PHE:plan': 5, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 167 Chain: "R" Number of atoms: 3335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 411, 3335 Classifications: {'peptide': 411} Link IDs: {'PTRANS': 25, 'TRANS': 385} Chain breaks: 1 Chain: "S" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1695 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 10, 'TRANS': 197} Chain breaks: 3 Chain: "T" Number of atoms: 3391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3391 Classifications: {'peptide': 443} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 18, 'TRANS': 424} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "U" Number of atoms: 3299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 430, 3299 Classifications: {'peptide': 430} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 419} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "V" Number of atoms: 3336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3336 Classifications: {'peptide': 434} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 17, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "W" Number of atoms: 3325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3325 Classifications: {'peptide': 433} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 10, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "X" Number of atoms: 3397 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3397 Classifications: {'peptide': 442} Link IDs: {'PTRANS': 18, 'TRANS': 423} Chain: "Y" Number of atoms: 3410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 447, 3410 Classifications: {'peptide': 447} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 10, 'TRANS': 436} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "M" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "Y" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 29 Unusual residues: {' MG': 2, 'ADP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 23819 SG CYS S 244 49.911 70.845 117.679 1.00 74.04 S ATOM 23839 SG CYS S 247 46.584 68.555 114.591 1.00 61.50 S ATOM 23955 SG CYS S 264 47.615 71.995 114.554 1.00 90.14 S ATOM 23980 SG CYS S 268 45.500 71.489 117.455 1.00 85.21 S ATOM 23899 SG CYS S 256 52.142 78.661 124.394 1.00 96.12 S ATOM 23920 SG CYS S 259 53.977 75.901 126.523 1.00 80.86 S ATOM 24059 SG CYS S 277 50.955 77.008 128.993 1.00111.59 S Time building chain proxies: 23.01, per 1000 atoms: 0.52 Number of scatterers: 44481 At special positions: 0 Unit cell: (169.83, 199.8, 206.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 2 29.99 S 118 16.00 P 362 15.00 Mg 8 11.99 F 6 9.00 O 9204 8.00 N 7881 7.00 C 26898 6.00 Be 2 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 18.41 Conformation dependent library (CDL) restraints added in 6.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN S 501 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 264 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 244 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 268 " pdb="ZN ZN S 501 " - pdb=" SG CYS S 247 " pdb=" ZN S 502 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 259 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 277 " pdb="ZN ZN S 502 " - pdb=" SG CYS S 256 " pdb="ZN ZN S 502 " - pdb=" NE2 HIS S 272 " Number of angles added : 9 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9030 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 195 helices and 34 sheets defined 42.6% alpha, 10.3% beta 167 base pairs and 294 stacking pairs defined. Time for finding SS restraints: 32.84 Creating SS restraints... Processing helix chain 'Z' and resid 102 through 128 Processing helix chain 'Z' and resid 137 through 141 Processing helix chain 'A' and resid 46 through 54 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 90 through 113 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'B' and resid 46 through 54 Processing helix chain 'B' and resid 64 through 74 Processing helix chain 'B' and resid 90 through 113 Processing helix chain 'B' and resid 121 through 129 Processing helix chain 'C' and resid 26 through 28 No H-bonds generated for 'chain 'C' and resid 26 through 28' Processing helix chain 'C' and resid 31 through 40 Processing helix chain 'C' and resid 50 through 75 removed outlier: 3.518A pdb=" N GLU C 63 " --> pdb=" O LYS C 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP C 68 " --> pdb=" O SER C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 83 through 89 Processing helix chain 'D' and resid 26 through 28 No H-bonds generated for 'chain 'D' and resid 26 through 28' Processing helix chain 'D' and resid 31 through 40 Processing helix chain 'D' and resid 50 through 75 removed outlier: 3.517A pdb=" N GLU D 63 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N ASP D 68 " --> pdb=" O SER D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 89 Processing helix chain 'E' and resid 18 through 21 No H-bonds generated for 'chain 'E' and resid 18 thr------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5895 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 45872 Z= 0.218 Angle : 0.755 14.190 63556 Z= 0.434 Chirality : 0.043 0.225 7440 Planarity : 0.005 0.082 6874 Dihedral : 20.637 178.540 17991 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.95 % Favored : 96.01 % Rotamer: Outliers : 8.77 % Allowed : 8.39 % Favored : 82.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.63 % Twisted General : 0.38 % 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: -4.51 (0.09), residues: 4633 helix: -3.92 (0.05), residues: 2130 sheet: -0.77 (0.20), residues: 580 loop : -2.36 (0.12), residues: 1923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 790 HIS 0.007 0.001 HIS U 153 PHE 0.014 0.001 PHE M1047 TYR 0.029 0.001 TYR V 462 ARG 0.004 0.000 ARG Y 208 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9266 Ramachandran restraints generated. 4633 Oldfield, 0 Emsley, 4633 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1505 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1155 time to evaluate : 4.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 ILE cc_start: 0.4546 (mt) cc_final: 0.4318 (mt) REVERT: B 131 ARG cc_start: 0.8259 (mtp180) cc_final: 0.7979 (mtp85) REVERT: C 70 VAL cc_start: 0.8574 (t) cc_final: 0.8324 (t) REVERT: C 78 ARG cc_start: 0.6949 (mtt180) cc_final: 0.6618 (ttm-80) REVERT: D 67 ARG cc_start: 0.8364 (tpt-90) cc_final: 0.8151 (ttp-110) REVERT: E 57 GLU cc_start: 0.7603 (tt0) cc_final: 0.6651 (tt0) REVERT: F 93 GLU cc_start: 0.8648 (mp0) cc_final: 0.8428 (mp0) REVERT: F 94 LEU cc_start: 0.8695 (mt) cc_final: 0.8450 (mt) REVERT: H 72 ILE cc_start: 0.8832 (mm) cc_final: 0.8344 (mm) REVERT: M 794 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.7227 (p0) REVERT: M 937 VAL cc_start: 0.7061 (OUTLIER) cc_final: 0.6812 (t) REVERT: M 1039 ASP cc_start: 0.7924 (t70) cc_final: 0.7482 (t0) REVERT: M 1054 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7332 (tp) REVERT: M 1082 ASN cc_start: 0.6472 (OUTLIER) cc_final: 0.6088 (m-40) REVERT: M 1192 MET cc_start: 0.6490 (tpt) cc_final: 0.6277 (tpt) REVERT: M 1326 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7638 (tp) REVERT: R 226 LEU cc_start: 0.8111 (tp) cc_final: 0.7689 (tp) REVERT: R 230 THR cc_start: 0.7902 (p) cc_final: 0.7674 (t) REVERT: R 408 SER cc_start: 0.8927 (m) cc_final: 0.8687 (t) REVERT: S 12 THR cc_start: 0.8160 (m) cc_final: 0.7783 (m) REVERT: S 49 ILE cc_start: 0.7094 (mt) cc_final: 0.6619 (mm) REVERT: S 175 ILE cc_start: 0.8726 (mt) cc_final: 0.8508 (pt) REVERT: S 278 ARG cc_start: 0.5531 (mmt-90) cc_final: 0.5088 (tpm170) REVERT: T 133 ILE cc_start: -0.3733 (OUTLIER) cc_final: -0.4011 (mt) REVERT: T 182 ASP cc_start: 0.3031 (OUTLIER) cc_final: 0.2649 (t70) REVERT: T 202 ILE cc_start: 0.5247 (OUTLIER) cc_final: 0.4849 (tt) REVERT: T 226 THR cc_start: 0.5115 (OUTLIER) cc_final: 0.4731 (t) REVERT: T 233 PRO cc_start: 0.0224 (Cg_exo) cc_final: -0.0106 (Cg_endo) REVERT: T 456 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6732 (tp) REVERT: U 15 LYS cc_start: 0.6000 (OUTLIER) cc_final: 0.4993 (tptp) REVERT: U 136 ILE cc_start: 0.7432 (mt) cc_final: 0.7107 (tp) REVERT: U 252 GLN cc_start: 0.4484 (OUTLIER) cc_final: 0.3094 (tt0) REVERT: U 259 THR cc_start: 0.6839 (p) cc_final: 0.6277 (p) REVERT: V 24 THR cc_start: 0.7758 (m) cc_final: 0.7356 (p) REVERT: V 247 VAL cc_start: 0.8180 (OUTLIER) cc_final: 0.7964 (p) REVERT: V 317 ASP cc_start: 0.8497 (t0) cc_final: 0.8261 (t70) REVERT: W 160 ILE cc_start: 0.8608 (mt) cc_final: 0.8272 (tp) REVERT: W 255 LEU cc_start: 0.8307 (mt) cc_final: 0.7946 (tp) REVERT: W 420 VAL cc_start: 0.6609 (OUTLIER) cc_final: 0.6051 (t) REVERT: X 153 GLU cc_start: 0.7259 (OUTLIER) cc_final: 0.6959 (pm20) REVERT: X 162 THR cc_start: -0.0253 (OUTLIER) cc_final: -0.1005 (p) REVERT: X 163 ILE cc_start: 0.0102 (OUTLIER) cc_final: -0.0589 (mt) REVERT: Y 117 LEU cc_start: 0.7518 (tp) cc_final: 0.7225 (tp) REVERT: Y 135 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.6982 (tt) REVERT: Y 160 ILE cc_start: 0.8727 (mt) cc_final: 0.8509 (tp) REVERT: Y 268 GLU cc_start: 0.2285 (OUTLIER) cc_final: -0.0625 (mm-30) REVERT: Y 456 ILE cc_start: 0.0232 (OUTLIER) cc_final: -0.0087 (pt) outliers start: 350 outliers final: 41 residues processed: 1423 average time/residue: 0.6246 time to fit residues: 1420.3360 Evaluate side-chains 560 residues out of total 4069 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 499 time to evaluate : 4.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 92 ARG Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain G residue 103 LEU Chi-restraints excluded: chain H residue 103 LEU Chi-restraints excluded: chain M residue 794 ASP Chi-restraints excluded: chain M residue 937 VAL Chi-restraints excluded: chain M residue 999 PHE Chi-restraints excluded: chain M residue 1038 VAL Chi-restraints excluded: chain M residue 1046 VAL Chi-restraints excluded: chain M residue 1054 LEU Chi-restraints excluded: chain M residue 1055 THR Chi-restraints excluded: chain M residue 1066 THR Chi-restraints excluded: chain M residue 1068 VAL Chi-restraints excluded: chain M residue 1075 VAL Chi-restraints excluded: chain M residue 1082 ASN Chi-restraints excluded: chain M residue 1213 VAL Chi-restraints excluded: chain M residue 1274 VAL Chi-restraints excluded: chain M residue 1326 LEU Chi-restraints excluded: chain M residue 1386 LYS Chi-restraints excluded: chain M residue 1392 VAL Chi-restraints excluded: chain R residue 133 VAL Chi-restraints excluded: chain R residue 331 VAL Chi-restraints excluded: chain S residue 107 THR Chi-restraints excluded: chain S residue 266 VAL Chi-restraints excluded: chain T residue 49 VAL Chi-restraints excluded: chain T residue 133 ILE Chi-restraints excluded: chain T residue 159 TYR Chi-restraints excluded: chain T residue 182 ASP Chi-restraints excluded: chain T residue 202 ILE Chi-restraints excluded: chain T residue 226 THR Chi-restraints excluded: chain T residue 247 VAL Chi-restraints excluded: chain T residue 322 THR Chi-restraints excluded: chain T residue 456 LEU Chi-restraints excluded: chain U residue 15 LYS Chi-restraints excluded: chain U residue 118 THR Chi-restraints excluded: chain U residue 149 ILE Chi-restraints excluded: chain U residue 191 SER Chi-restraints excluded: chain U residue 252 GLN Chi-restraints excluded: chain U residue 273 ILE Chi-restraints excluded: chain V residue 247 VAL Chi-restraints excluded: chain V residue 278 THR Chi-restraints excluded: chain V residue 292 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 206 PHE Chi-restraints excluded: chain W residue 339 SER Chi-restraints excluded: chain W residue 352 ILE Chi-restraints excluded: chain W residue 420 VAL Chi-restraints excluded: chain X residue 153 GLU Chi-restraints excluded: chain X residue 162 THR Chi-restraints excluded: chain X residue 163 ILE Chi-restraints excluded: chain X residue 244 VAL Chi-restraints excluded: chain Y residue 14 LEU Chi-restraints excluded: chain Y residue 135 LEU Chi-restraints excluded: chain Y residue 202 LEU Chi-restraints excluded: chain Y residue 219 THR Chi-restraints excluded: chain Y residue 221 PHE Chi-restraints excluded: chain Y residue 236 VAL Chi-restraints excluded: chain Y residue 268 GLU Chi-restraints excluded: chain Y residue 320 ILE Chi-restraints excluded: chain Y residue 396 LEU Chi-restraints excluded: chain Y residue 456 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 509 random chunks: chunk 429 optimal weight: 7.9990 chunk 385 optimal weight: 0.6980 chunk 214 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 260 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 398 optimal weight: 20.0000 chunk 154 optimal weight: 7.9990 chunk 242 optimal weight: 5.9990 chunk 296 optimal weight: 0.8980 chunk 462 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: