Starting phenix.real_space_refine on Sat Mar 23 01:56:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v8a_43032/03_2024/8v8a_43032_trim_updated.pdb" } resolution = 2.19 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= 0.125 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: 8 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 120 5.16 5 Cl 10 4.86 5 C 11510 2.51 5 N 2650 2.21 5 O 3315 1.98 5 H 15935 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 33560 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6391 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6370 Chain: "B" Number of atoms: 6391 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6370 Chain: "C" Number of atoms: 6391 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6370 Chain: "D" Number of atoms: 6391 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6370 Chain: "E" Number of atoms: 6391 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6340 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 394, 6341 Classifications: {'peptide': 394} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 372} Chain breaks: 1 bond proxies already assigned to first conformer: 6370 Chain: "F" 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: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" 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: "I" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 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: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "L" 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: "M" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" 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: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 223 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'I34': 1, 'NAG': 1, 'POV': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Classifications: {'water': 31} Link IDs: {None: 30} Time building chain proxies: 26.24, per 1000 atoms: 0.78 Number of scatterers: 33560 At special positions: 0 Unit cell: (99, 101.475, 163.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Ca 5 19.99 Cl 10 17.00 S 120 16.00 P 15 15.00 O 3315 8.00 N 2650 7.00 C 11510 6.00 H 15935 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 127 " - pdb=" SG CYS A 141 " distance=2.04 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.05 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.04 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.05 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.04 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.05 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.04 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.05 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.04 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.05 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG I 2 " - " BMA I 3 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG K 2 " - " BMA K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " NAG-ASN " NAG A 602 " - " ASN A 67 " " NAG B 604 " - " ASN B 67 " " NAG C 604 " - " ASN C 67 " " NAG D 604 " - " ASN D 67 " " NAG E 604 " - " ASN E 67 " " NAG F 1 " - " ASN A 23 " " NAG G 1 " - " ASN A 110 " " NAG H 1 " - " ASN B 23 " " NAG I 1 " - " ASN B 110 " " NAG J 1 " - " ASN C 23 " " NAG K 1 " - " ASN C 110 " " NAG L 1 " - " ASN D 23 " " NAG M 1 " - " ASN D 110 " " NAG N 1 " - " ASN E 23 " " NAG O 1 " - " ASN E 110 " Time building additional restraints: 27.78 Conformation dependent library (CDL) restraints added in 6.2 seconds 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3800 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 25 sheets defined 40.6% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.01 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.809A pdb=" N ALA A 225 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU A 226 " --> pdb=" O SER A 222 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU A 230 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 238 through 258 removed outlier: 3.779A pdb=" N THR A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET A 253 " --> pdb=" O LEU A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 295 Processing helix chain 'A' and resid 306 through 311 Processing helix chain 'A' and resid 315 through 319 Processing helix chain 'A' and resid 409 through 466 Processing helix chain 'A' and resid 470 through 477 Processing helix chain 'B' and resid 2 through 11 Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 230 removed outlier: 3.809A pdb=" N ALA B 225 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LEU B 226 " --> pdb=" O SER B 222 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 235 No H-bonds generated for 'chain 'B' and resid 233 through 235' Processing helix chain 'B' and resid 238 through 258 removed outlier: 3.779A pdb=" N THR B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 295 Processing helix chain 'B' and resid 306 through 311 Processing helix chain 'B' and resid 315 through 319 Processing helix chain 'B' and resid 409 through 466 Processing helix chain 'B' and resid 470 through 477 Processing helix chain 'C' and resid 2 through 11 Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 230 removed outlier: 3.809A pdb=" N ALA C 225 " --> pdb=" O ILE C 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU C 226 " --> pdb=" O SER C 222 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU C 230 " --> pdb=" O LEU C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 235 No H-bonds generated for 'chain 'C' and resid 233 through 235' Processing helix chain 'C' and resid 238 through 258 removed outlier: 3.779A pdb=" N THR C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET C 253 " --> pdb=" O LEU C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 295 Processing helix chain 'C' and resid 306 through 311 Processing helix chain 'C' and resid 315 through 319 Processing helix chain 'C' and resid 409 through 466 Processing helix chain 'C' and resid 470 through 477 Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 230 removed outlier: 3.809A pdb=" N ALA D 225 " --> pdb=" O ILE D 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU D 226 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU D 230 " --> pdb=" O LEU D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 235 No H-bonds generated for 'chain 'D' and resid 233 through 235' Processing helix chain 'D' and resid 238 through 258 removed outlier: 3.779A pdb=" N THR D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET D 253 " --> pdb=" O LEU D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 295 Processing helix chain 'D' and resid 306 through 311 Processing helix chain 'D' and resid 315 through 319 Processing helix chain 'D' and resid 409 through 466 Processing helix chain 'D' and resid 470 through 477 Processing helix chain 'E' and resid 2 through 11 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 230 removed outlier: 3.809A pdb=" N ALA E 225 " --> pdb=" O ILE E 221 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU E 226 " --> pdb=" O SER E 222 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU E 230 " --> pdb=" O LEU E 226 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 235 No H-bonds generated for 'chain 'E' and resid 233 through 235' Processing helix chain 'E' and resid 238 through 258 removed outlier: 3.779A pdb=" N THR E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N MET E 253 " --> pdb=" O LEU E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 295 Processing helix chain 'E' and resid 306 through 311 Processing helix chain 'E' and resid 315 through 319 Processing helix chain 'E' and resid 409 through 466 Processing helix chain 'E' and resid 470 through 477 Processing sheet with id= A, first strand: chain 'A' and resid 155 through 159 removed outlier: 6.155A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 41 through 43 Processing sheet with id= C, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= D, first strand: chain 'A' and resid 76 through 79 Processing sheet with id= E, first strand: chain 'A' and resid 89 through 91 removed outlier: 4.420A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG A 185 " --> pdb=" O TYR A 194 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 177 " --> pdb=" O THR A 202 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU A 175 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 155 through 159 removed outlier: 6.155A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR B 50 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 41 through 43 Processing sheet with id= H, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'B' and resid 76 through 79 Processing sheet with id= J, first strand: chain 'B' and resid 89 through 91 removed outlier: 4.419A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG B 185 " --> pdb=" O TYR B 194 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY B 177 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.304A pdb=" N LEU B 175 " --> pdb=" O ARG B 204 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 155 through 159 removed outlier: 6.155A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 41 through 43 Processing sheet with id= M, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= N, first strand: chain 'C' and resid 76 through 79 Processing sheet with id= O, first strand: chain 'C' and resid 89 through 91 removed outlier: 4.420A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ARG C 185 " --> pdb=" O TYR C 194 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY C 177 " --> pdb=" O THR C 202 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU C 175 " --> pdb=" O ARG C 204 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 155 through 159 removed outlier: 6.155A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N THR D 50 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'D' and resid 41 through 43 Processing sheet with id= R, first strand: chain 'D' and resid 57 through 60 Processing sheet with id= S, first strand: chain 'D' and resid 76 through 79 Processing sheet with id= T, first strand: chain 'D' and resid 89 through 91 removed outlier: 4.420A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG D 185 " --> pdb=" O TYR D 194 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY D 177 " --> pdb=" O THR D 202 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU D 175 " --> pdb=" O ARG D 204 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.155A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.115A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N THR E 50 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'E' and resid 41 through 43 Processing sheet with id= W, first strand: chain 'E' and resid 57 through 60 Processing sheet with id= X, first strand: chain 'E' and resid 76 through 79 Processing sheet with id= Y, first strand: chain 'E' and resid 89 through 91 removed outlier: 4.420A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ARG E 185 " --> pdb=" O TYR E 194 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY E 177 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2215 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: 12.72 Time building geometry restraints manager: 28.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.05: 15910 1.05 - 1.25: 2620 1.25 - 1.46: 6716 1.46 - 1.67: 8469 1.67 - 1.87: 190 Bond restraints: 33905 Sorted by residual: bond pdb=" C3 EPJ E 608 " pdb=" N1 EPJ E 608 " ideal model delta sigma weight residual 1.718 1.472 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C3 EPJ D 608 " pdb=" N1 EPJ D 608 " ideal model delta sigma weight residual 1.718 1.472 0.246 2.00e-02 2.50e+03 1.51e+02 bond pdb=" C3 EPJ A 606 " pdb=" N1 EPJ A 606 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C3 EPJ B 608 " pdb=" N1 EPJ B 608 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.50e+02 bond pdb=" C3 EPJ C 608 " pdb=" N1 EPJ C 608 " ideal model delta sigma weight residual 1.718 1.473 0.245 2.00e-02 2.50e+03 1.50e+02 ... (remaining 33900 not shown) Histogram of bond angle deviations from ideal: 95.61 - 103.33: 247 103.33 - 111.05: 34075 111.05 - 118.78: 11350 118.78 - 126.50: 14583 126.50 - 134.22: 425 Bond angle restraints: 60680 Sorted by residual: angle pdb=" C2 POV C 601 " pdb=" O21 POV C 601 " pdb=" C21 POV C 601 " ideal model delta sigma weight residual 119.46 131.19 -11.73 3.00e+00 1.11e-01 1.53e+01 angle pdb=" C2 POV B 601 " pdb=" O21 POV B 601 " pdb=" C21 POV B 601 " ideal model delta sigma weight residual 119.46 131.18 -11.72 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C2 POV D 601 " pdb=" O21 POV D 601 " pdb=" C21 POV D 601 " ideal model delta sigma weight residual 119.46 131.17 -11.71 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C2 POV A 607 " pdb=" O21 POV A 607 " pdb=" C21 POV A 607 " ideal model delta sigma weight residual 119.46 131.16 -11.70 3.00e+00 1.11e-01 1.52e+01 angle pdb=" C2 POV E 601 " pdb=" O21 POV E 601 " pdb=" C21 POV E 601 " ideal model delta sigma weight residual 119.46 131.16 -11.70 3.00e+00 1.11e-01 1.52e+01 ... (remaining 60675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.55: 16176 29.55 - 59.11: 754 59.11 - 88.66: 95 88.66 - 118.22: 45 118.22 - 147.77: 15 Dihedral angle restraints: 17085 sinusoidal: 9850 harmonic: 7235 Sorted by residual: dihedral pdb=" CA CYS B 189 " pdb=" C CYS B 189 " pdb=" N CYS B 190 " pdb=" CA CYS B 190 " ideal model delta harmonic sigma weight residual -180.00 -153.87 -26.13 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS C 189 " pdb=" C CYS C 189 " pdb=" N CYS C 190 " pdb=" CA CYS C 190 " ideal model delta harmonic sigma weight residual -180.00 -153.88 -26.12 0 5.00e+00 4.00e-02 2.73e+01 dihedral pdb=" CA CYS A 189 " pdb=" C CYS A 189 " pdb=" N CYS A 190 " pdb=" CA CYS A 190 " ideal model delta harmonic sigma weight residual -180.00 -153.89 -26.11 0 5.00e+00 4.00e-02 2.73e+01 ... (remaining 17082 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 2112 0.064 - 0.127: 528 0.127 - 0.191: 80 0.191 - 0.254: 35 0.254 - 0.318: 5 Chirality restraints: 2760 Sorted by residual: chirality pdb=" C1 BMA I 3 " pdb=" O4 NAG I 2 " pdb=" C2 BMA I 3 " pdb=" O5 BMA I 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.76e+01 chirality pdb=" C1 BMA G 3 " pdb=" O4 NAG G 2 " pdb=" C2 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.59e+01 chirality pdb=" C1 BMA O 3 " pdb=" O4 NAG O 2 " pdb=" C2 BMA O 3 " pdb=" O5 BMA O 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.24 -0.16 2.00e-02 2.50e+03 6.54e+01 ... (remaining 2757 not shown) Planarity restraints: 4775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN D 427 " 0.073 2.00e-02 2.50e+03 6.31e-02 5.98e+01 pdb=" CD GLN D 427 " -0.081 2.00e-02 2.50e+03 pdb=" OE1 GLN D 427 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN D 427 " -0.008 2.00e-02 2.50e+03 pdb="HE21 GLN D 427 " -0.060 2.00e-02 2.50e+03 pdb="HE22 GLN D 427 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN C 427 " 0.073 2.00e-02 2.50e+03 6.31e-02 5.98e+01 pdb=" CD GLN C 427 " -0.081 2.00e-02 2.50e+03 pdb=" OE1 GLN C 427 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN C 427 " -0.009 2.00e-02 2.50e+03 pdb="HE21 GLN C 427 " -0.060 2.00e-02 2.50e+03 pdb="HE22 GLN C 427 " 0.090 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN E 427 " 0.073 2.00e-02 2.50e+03 6.31e-02 5.97e+01 pdb=" CD GLN E 427 " -0.081 2.00e-02 2.50e+03 pdb=" OE1 GLN E 427 " -0.013 2.00e-02 2.50e+03 pdb=" NE2 GLN E 427 " -0.009 2.00e-02 2.50e+03 pdb="HE21 GLN E 427 " -0.060 2.00e-02 2.50e+03 pdb="HE22 GLN E 427 " 0.090 2.00e-02 2.50e+03 ... (remaining 4772 not shown) Histogram of nonbonded interaction distances: 1.54 - 2.15: 993 2.15 - 2.76: 60959 2.76 - 3.38: 97168 3.38 - 3.99: 132429 3.99 - 4.60: 200062 Nonbonded interactions: 491611 Sorted by model distance: nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.541 2.100 nonbonded pdb=" HZ1 LYS B 144 " pdb=" HH TYR B 187 " model vdw 1.541 2.100 nonbonded pdb=" HZ1 LYS A 144 " pdb=" HH TYR A 187 " model vdw 1.541 2.100 nonbonded pdb=" HZ1 LYS D 144 " pdb=" HH TYR D 187 " model vdw 1.541 2.100 nonbonded pdb=" HZ1 LYS C 144 " pdb=" HH TYR C 187 " model vdw 1.541 2.100 ... (remaining 491606 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) selection = (chain 'B' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) selection = (chain 'D' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) selection = (chain 'E' and (resid 1 through 55 or resid 57 through 83 or resid 85 through 11 \ 3 or resid 115 through 252 or resid 254 through 478)) } ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 1.760 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: 0.510 Extract box with map and model: 8.830 Check model and map are aligned: 0.530 Set scattering table: 0.320 Process input model: 123.100 Find NCS groups from input model: 1.630 Set up NCS constraints: 0.250 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 149.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.012 0.246 17955 Z= 0.695 Angle : 1.162 11.726 24410 Z= 0.561 Chirality : 0.059 0.318 2760 Planarity : 0.007 0.052 2890 Dihedral : 19.814 147.774 7655 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.56 % Allowed : 0.28 % Favored : 99.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: -0.64 (0.17), residues: 1970 helix: -0.25 (0.16), residues: 790 sheet: -0.77 (0.21), residues: 490 loop : -0.00 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP D 153 HIS 0.009 0.004 HIS E 297 PHE 0.022 0.003 PHE E 99 TYR 0.018 0.004 TYR D 273 ARG 0.006 0.001 ARG E 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 270 time to evaluate : 2.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.7905 (mmt) cc_final: 0.7668 (mmt) REVERT: A 428 ASP cc_start: 0.7866 (m-30) cc_final: 0.7643 (m-30) REVERT: C 40 MET cc_start: 0.8089 (mtp) cc_final: 0.7848 (mtm) REVERT: C 454 VAL cc_start: 0.7964 (t) cc_final: 0.7751 (p) REVERT: E 57 MET cc_start: 0.8505 (mtm) cc_final: 0.8239 (mtp) outliers start: 5 outliers final: 5 residues processed: 275 average time/residue: 2.9099 time to fit residues: 890.3968 Evaluate side-chains 246 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 241 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 147 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 92 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 177 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN B 52 ASN B 272 GLN C 272 GLN D 52 ASN D 272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17955 Z= 0.199 Angle : 0.629 6.952 24410 Z= 0.317 Chirality : 0.042 0.178 2760 Planarity : 0.004 0.041 2890 Dihedral : 18.448 139.398 3870 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.11 % Allowed : 4.17 % Favored : 94.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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 (0.18), residues: 1970 helix: 1.15 (0.17), residues: 795 sheet: -0.52 (0.23), residues: 485 loop : 0.21 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 307 HIS 0.004 0.002 HIS A 62 PHE 0.014 0.002 PHE B 455 TYR 0.010 0.002 TYR C 273 ARG 0.006 0.000 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 253 time to evaluate : 2.452 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 40 MET cc_start: 0.8169 (mtp) cc_final: 0.7949 (mtm) REVERT: D 461 ILE cc_start: 0.8108 (OUTLIER) cc_final: 0.7859 (mp) REVERT: E 57 MET cc_start: 0.8502 (mtm) cc_final: 0.8222 (mtp) outliers start: 15 outliers final: 6 residues processed: 261 average time/residue: 2.6979 time to fit residues: 788.8960 Evaluate side-chains 244 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 237 time to evaluate : 2.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 461 ILE Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 147 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 177 optimal weight: 2.9990 chunk 191 optimal weight: 4.9990 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17955 Z= 0.242 Angle : 0.652 5.803 24410 Z= 0.331 Chirality : 0.044 0.260 2760 Planarity : 0.005 0.047 2890 Dihedral : 16.281 132.905 3870 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.11 % Allowed : 5.39 % Favored : 93.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.70 (0.18), residues: 1970 helix: 1.30 (0.17), residues: 805 sheet: -0.39 (0.23), residues: 480 loop : 0.34 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 148 HIS 0.007 0.002 HIS C 297 PHE 0.018 0.002 PHE A 99 TYR 0.014 0.002 TYR C 273 ARG 0.008 0.001 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 236 time to evaluate : 2.657 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.7995 (mmp) cc_final: 0.7715 (mmt) REVERT: E 57 MET cc_start: 0.8536 (mtm) cc_final: 0.8205 (mtp) REVERT: E 260 MET cc_start: 0.8256 (mmp) cc_final: 0.7898 (mmp) outliers start: 15 outliers final: 6 residues processed: 239 average time/residue: 2.8928 time to fit residues: 769.8219 Evaluate side-chains 235 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 229 time to evaluate : 2.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 175 optimal weight: 2.9990 chunk 133 optimal weight: 0.1980 chunk 92 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 119 optimal weight: 0.0470 chunk 178 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 93 optimal weight: 1.9990 chunk 168 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 overall best weight: 0.7880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17955 Z= 0.170 Angle : 0.548 6.387 24410 Z= 0.281 Chirality : 0.040 0.161 2760 Planarity : 0.004 0.043 2890 Dihedral : 15.048 131.827 3870 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.00 % Allowed : 5.44 % Favored : 93.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.92 (0.18), residues: 1970 helix: 1.57 (0.17), residues: 810 sheet: -0.39 (0.23), residues: 470 loop : 0.39 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 307 HIS 0.003 0.001 HIS B 295 PHE 0.011 0.001 PHE C 252 TYR 0.012 0.002 TYR A 273 ARG 0.006 0.000 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 230 time to evaluate : 2.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.8126 (mmp) cc_final: 0.7457 (mmp) REVERT: C 98 ARG cc_start: 0.7633 (OUTLIER) cc_final: 0.7059 (ptt90) REVERT: E 57 MET cc_start: 0.8516 (mtm) cc_final: 0.8229 (mtp) REVERT: E 445 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7020 (t0) outliers start: 13 outliers final: 6 residues processed: 231 average time/residue: 2.9044 time to fit residues: 747.7479 Evaluate side-chains 237 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 229 time to evaluate : 2.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 2 optimal weight: 0.0870 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 0.0170 chunk 130 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 169 optimal weight: 1.9990 chunk 47 optimal weight: 0.2980 overall best weight: 0.6800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17955 Z= 0.164 Angle : 0.537 6.690 24410 Z= 0.274 Chirality : 0.040 0.159 2760 Planarity : 0.004 0.045 2890 Dihedral : 14.542 129.276 3870 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.94 % Allowed : 5.83 % Favored : 93.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.94 (0.19), residues: 1970 helix: 1.68 (0.17), residues: 810 sheet: -0.51 (0.24), residues: 435 loop : 0.32 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 307 HIS 0.003 0.001 HIS B 296 PHE 0.011 0.001 PHE B 99 TYR 0.012 0.002 TYR A 273 ARG 0.008 0.000 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 232 time to evaluate : 2.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 260 MET cc_start: 0.8107 (mmp) cc_final: 0.7485 (mmt) REVERT: C 98 ARG cc_start: 0.7577 (OUTLIER) cc_final: 0.6975 (pmt100) REVERT: E 57 MET cc_start: 0.8516 (mtm) cc_final: 0.8234 (mtp) REVERT: E 445 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7033 (t0) outliers start: 12 outliers final: 6 residues processed: 232 average time/residue: 2.9258 time to fit residues: 756.5344 Evaluate side-chains 238 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 230 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 2.9990 chunk 169 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 110 optimal weight: 0.0770 chunk 46 optimal weight: 2.9990 chunk 188 optimal weight: 5.9990 chunk 156 optimal weight: 0.7980 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 GLN C 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17955 Z= 0.276 Angle : 0.648 6.239 24410 Z= 0.333 Chirality : 0.043 0.263 2760 Planarity : 0.005 0.055 2890 Dihedral : 14.757 127.753 3870 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.94 % Allowed : 5.94 % Favored : 93.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.87 (0.18), residues: 1970 helix: 1.51 (0.17), residues: 810 sheet: -0.41 (0.23), residues: 470 loop : 0.39 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 148 HIS 0.008 0.002 HIS C 297 PHE 0.022 0.002 PHE B 99 TYR 0.016 0.003 TYR A 273 ARG 0.008 0.001 ARG C 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 234 time to evaluate : 2.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 ARG cc_start: 0.7605 (OUTLIER) cc_final: 0.6975 (pmt100) REVERT: E 445 ASP cc_start: 0.7466 (OUTLIER) cc_final: 0.7043 (t0) outliers start: 12 outliers final: 6 residues processed: 234 average time/residue: 2.9768 time to fit residues: 772.4769 Evaluate side-chains 235 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 227 time to evaluate : 2.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 0.5980 chunk 158 optimal weight: 0.8980 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 17955 Z= 0.210 Angle : 0.581 6.594 24410 Z= 0.299 Chirality : 0.041 0.196 2760 Planarity : 0.004 0.046 2890 Dihedral : 14.290 125.282 3870 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.94 % Allowed : 6.11 % Favored : 92.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.90 (0.18), residues: 1970 helix: 1.57 (0.17), residues: 815 sheet: -0.37 (0.23), residues: 465 loop : 0.33 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 307 HIS 0.004 0.001 HIS B 296 PHE 0.016 0.002 PHE C 99 TYR 0.015 0.002 TYR A 273 ARG 0.008 0.001 ARG A 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 233 time to evaluate : 2.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7011 (ptt90) REVERT: C 98 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6916 (pmt100) REVERT: E 98 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.7110 (pmt100) REVERT: E 445 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7016 (t0) outliers start: 12 outliers final: 3 residues processed: 233 average time/residue: 3.0274 time to fit residues: 788.4356 Evaluate side-chains 235 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 228 time to evaluate : 2.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 2.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 0.0670 chunk 128 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 170 optimal weight: 2.9990 overall best weight: 2.4126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17955 Z= 0.348 Angle : 0.721 7.982 24410 Z= 0.370 Chirality : 0.046 0.274 2760 Planarity : 0.006 0.067 2890 Dihedral : 14.827 124.762 3870 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.83 % Allowed : 6.50 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.73 (0.18), residues: 1970 helix: 1.38 (0.17), residues: 810 sheet: -0.41 (0.22), residues: 470 loop : 0.28 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 148 HIS 0.009 0.003 HIS C 297 PHE 0.025 0.003 PHE B 99 TYR 0.018 0.003 TYR A 273 ARG 0.008 0.001 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 233 time to evaluate : 2.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 98 ARG cc_start: 0.7535 (OUTLIER) cc_final: 0.6922 (pmt100) REVERT: E 445 ASP cc_start: 0.7448 (OUTLIER) cc_final: 0.7013 (t0) outliers start: 10 outliers final: 5 residues processed: 233 average time/residue: 3.0206 time to fit residues: 780.8168 Evaluate side-chains 239 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 232 time to evaluate : 2.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 2.9990 chunk 164 optimal weight: 0.1980 chunk 175 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17955 Z= 0.193 Angle : 0.574 7.106 24410 Z= 0.295 Chirality : 0.040 0.186 2760 Planarity : 0.004 0.051 2890 Dihedral : 14.188 122.780 3870 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.72 % Allowed : 6.78 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 0.87 (0.18), residues: 1970 helix: 1.56 (0.17), residues: 815 sheet: -0.37 (0.23), residues: 465 loop : 0.27 (0.23), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 307 HIS 0.003 0.001 HIS B 295 PHE 0.014 0.001 PHE C 99 TYR 0.015 0.002 TYR A 273 ARG 0.008 0.000 ARG B 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 234 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.7636 (OUTLIER) cc_final: 0.7014 (ptt90) REVERT: C 98 ARG cc_start: 0.7488 (OUTLIER) cc_final: 0.6857 (pmt100) REVERT: D 98 ARG cc_start: 0.7513 (OUTLIER) cc_final: 0.7074 (pmt100) REVERT: E 445 ASP cc_start: 0.7439 (OUTLIER) cc_final: 0.7025 (t0) outliers start: 8 outliers final: 3 residues processed: 234 average time/residue: 3.0200 time to fit residues: 783.9108 Evaluate side-chains 243 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 185 optimal weight: 2.9990 chunk 113 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 194 optimal weight: 0.9990 chunk 178 optimal weight: 3.9990 chunk 154 optimal weight: 0.2980 chunk 16 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 94 optimal weight: 0.1980 chunk 122 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17955 Z= 0.160 Angle : 0.528 7.679 24410 Z= 0.270 Chirality : 0.039 0.163 2760 Planarity : 0.004 0.058 2890 Dihedral : 13.533 114.876 3870 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.67 % Allowed : 7.00 % Favored : 92.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.09 (0.19), residues: 1970 helix: 1.84 (0.17), residues: 810 sheet: -0.42 (0.23), residues: 445 loop : 0.36 (0.23), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS C 297 PHE 0.009 0.001 PHE D 99 TYR 0.014 0.001 TYR A 273 ARG 0.009 0.000 ARG B 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3940 Ramachandran restraints generated. 1970 Oldfield, 0 Emsley, 1970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 236 time to evaluate : 2.570 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 98 ARG cc_start: 0.7567 (OUTLIER) cc_final: 0.6990 (ptt90) REVERT: C 98 ARG cc_start: 0.7434 (OUTLIER) cc_final: 0.6916 (pmt100) REVERT: E 445 ASP cc_start: 0.7460 (OUTLIER) cc_final: 0.7068 (t0) outliers start: 7 outliers final: 4 residues processed: 236 average time/residue: 2.9623 time to fit residues: 779.3377 Evaluate side-chains 239 residues out of total 1760 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 232 time to evaluate : 2.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain B residue 98 ARG Chi-restraints excluded: chain C residue 98 ARG Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 98 ARG Chi-restraints excluded: chain E residue 98 ARG Chi-restraints excluded: chain E residue 445 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 142 optimal weight: 0.0980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 159 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 136 optimal weight: 0.8980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.169608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.147342 restraints weight = 56040.379| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 0.84 r_work: 0.3386 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3245 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3245 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3219 r_free = 0.3219 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3219 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 17955 Z= 0.158 Angle : 0.530 6.297 24410 Z= 0.271 Chirality : 0.039 0.164 2760 Planarity : 0.004 0.057 2890 Dihedral : 13.324 112.426 3870 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.67 % Allowed : 7.17 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % 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: 1.10 (0.19), residues: 1970 helix: 1.88 (0.17), residues: 810 sheet: -0.46 (0.24), residues: 435 loop : 0.34 (0.23), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.003 0.001 HIS C 296 PHE 0.010 0.001 PHE E 99 TYR 0.013 0.001 TYR A 273 ARG 0.009 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12658.89 seconds wall clock time: 222 minutes 51.98 seconds (13371.98 seconds total)