Starting phenix.real_space_refine on Mon Apr 15 10:50:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8v88_43030/04_2024/8v88_43030_trim_updated.pdb" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.013 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: 9 Type Number sf(0) Gaussians Ca 5 9.91 5 Br 5 7.06 5 P 10 5.49 5 S 120 5.16 5 Cl 5 4.86 5 C 11330 2.51 5 N 2640 2.21 5 O 3210 1.98 5 H 15865 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 184": "OE1" <-> "OE2" Residue "B GLU 184": "OE1" <-> "OE2" Residue "C GLU 184": "OE1" <-> "OE2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "E GLU 184": "OE1" <-> "OE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 33190 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 Chain: "B" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 Chain: "C" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 Chain: "D" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 Chain: "E" Number of atoms: 6367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 394, 6342 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, 6343 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: 6401 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: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 231 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 3, 'YLI': 1} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 184 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 184 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 184 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 2, 'YLI': 1} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 137 Unusual residues: {' CA': 1, '9Z9': 1, 'EPJ': 1, 'NAG': 1, 'POV': 1, 'YLI': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "B" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Time building chain proxies: 27.06, per 1000 atoms: 0.82 Number of scatterers: 33190 At special positions: 0 Unit cell: (100.347, 101.426, 166.166, 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) Br 5 34.99 Ca 5 19.99 Cl 5 17.00 S 120 16.00 P 10 15.00 O 3210 8.00 N 2640 7.00 C 11330 6.00 H 15865 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=2.03 Simple disulfide: pdb=" SG CYS A 189 " - pdb=" SG CYS A 190 " distance=2.04 Simple disulfide: pdb=" SG CYS B 127 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS B 189 " - pdb=" SG CYS B 190 " distance=2.04 Simple disulfide: pdb=" SG CYS C 127 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 189 " - pdb=" SG CYS C 190 " distance=2.04 Simple disulfide: pdb=" SG CYS D 127 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 189 " - pdb=" SG CYS D 190 " distance=2.04 Simple disulfide: pdb=" SG CYS E 127 " - pdb=" SG CYS E 141 " distance=2.03 Simple disulfide: pdb=" SG CYS E 189 " - pdb=" SG CYS E 190 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " 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 502 " - " ASN A 67 " " NAG B 502 " - " ASN B 67 " " NAG C 502 " - " ASN C 67 " " NAG D 502 " - " ASN D 67 " " NAG E 502 " - " 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: 26.81 Conformation dependent library (CDL) restraints added in 7.9 seconds 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 25 sheets defined 40.7% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.22 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 3.504A pdb=" N VAL A 11 " --> pdb=" O TYR A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.792A pdb=" N LEU A 227 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) removed outlier: 4.337A 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 259 removed outlier: 3.636A pdb=" N THR A 250 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL A 251 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (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 removed outlier: 3.503A pdb=" N VAL B 11 " --> pdb=" O TYR B 7 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 215 through 230 removed outlier: 3.792A pdb=" N LEU B 227 " --> pdb=" O ALA B 223 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N VAL B 228 " --> pdb=" O LEU B 224 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) removed outlier: 4.337A 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 259 removed outlier: 3.636A pdb=" N THR B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N VAL B 251 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (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 removed outlier: 3.504A pdb=" N VAL C 11 " --> pdb=" O TYR C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 213 Processing helix chain 'C' and resid 215 through 230 removed outlier: 3.792A pdb=" N LEU C 227 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL C 228 " --> pdb=" O LEU C 224 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) removed outlier: 4.337A 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 259 removed outlier: 3.636A pdb=" N THR C 250 " --> pdb=" O LEU C 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL C 251 " --> pdb=" O LEU C 247 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE C 252 " --> pdb=" O SER C 248 " (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 removed outlier: 3.503A pdb=" N VAL D 11 " --> pdb=" O TYR D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 215 through 229 removed outlier: 3.792A pdb=" N LEU D 227 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL D 228 " --> pdb=" O LEU D 224 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N PHE D 229 " --> pdb=" O ALA D 225 " (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 259 removed outlier: 3.636A pdb=" N THR D 250 " --> pdb=" O LEU D 246 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL D 251 " --> pdb=" O LEU D 247 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N PHE D 252 " --> pdb=" O SER D 248 " (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 10 Processing helix chain 'E' and resid 208 through 213 Processing helix chain 'E' and resid 215 through 229 removed outlier: 3.792A pdb=" N LEU E 227 " --> pdb=" O ALA E 223 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N VAL E 228 " --> pdb=" O LEU E 224 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N PHE E 229 " --> pdb=" O ALA E 225 " (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 259 removed outlier: 3.636A pdb=" N THR E 250 " --> pdb=" O LEU E 246 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL E 251 " --> pdb=" O LEU E 247 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N PHE E 252 " --> pdb=" O SER E 248 " (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: 6.309A pdb=" N LEU A 28 " --> pdb=" O ASP A 156 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN A 158 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL A 30 " --> pdb=" O GLN A 158 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN A 52 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE A 39 " --> pdb=" O THR A 50 " (cutoff:3.500A) removed outlier: 7.360A 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: 4.580A pdb=" N SER A 147 " --> pdb=" O PRO A 195 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG A 204 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 5.416A 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: 6.309A pdb=" N LEU B 28 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN B 158 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL B 30 " --> pdb=" O GLN B 158 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN B 52 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE B 39 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 7.361A 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: 4.581A pdb=" N SER B 147 " --> pdb=" O PRO B 195 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG B 204 " --> pdb=" O LEU B 175 " (cutoff:3.500A) removed outlier: 5.415A 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: 6.308A pdb=" N LEU C 28 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN C 158 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL C 30 " --> pdb=" O GLN C 158 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ASN C 52 " --> pdb=" O LEU C 37 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE C 39 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 7.361A 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: 4.580A pdb=" N SER C 147 " --> pdb=" O PRO C 195 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ARG C 204 " --> pdb=" O LEU C 175 " (cutoff:3.500A) removed outlier: 5.415A 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: 6.308A pdb=" N LEU D 28 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N GLN D 158 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL D 30 " --> pdb=" O GLN D 158 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASN D 52 " --> pdb=" O LEU D 37 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE D 39 " --> pdb=" O THR D 50 " (cutoff:3.500A) removed outlier: 7.360A 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: 4.580A pdb=" N SER D 147 " --> pdb=" O PRO D 195 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG D 204 " --> pdb=" O LEU D 175 " (cutoff:3.500A) removed outlier: 5.416A 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: 6.309A pdb=" N LEU E 28 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLN E 158 " --> pdb=" O LEU E 28 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL E 30 " --> pdb=" O GLN E 158 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN E 52 " --> pdb=" O LEU E 37 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE E 39 " --> pdb=" O THR E 50 " (cutoff:3.500A) removed outlier: 7.361A 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: 4.581A pdb=" N SER E 147 " --> pdb=" O PRO E 195 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ARG E 204 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N LEU E 175 " --> pdb=" O ARG E 204 " (cutoff:3.500A) 790 hydrogen bonds defined for protein. 2290 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: 13.93 Time building geometry restraints manager: 27.55 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: 15835 1.05 - 1.26: 2610 1.26 - 1.47: 7223 1.47 - 1.69: 7737 1.69 - 1.90: 185 Bond restraints: 33590 Sorted by residual: bond pdb=" C4 YLI B 507 " pdb=" C9 YLI B 507 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 bond pdb=" C4 YLI A 507 " pdb=" C9 YLI A 507 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 bond pdb=" C4 YLI D 507 " pdb=" C9 YLI D 507 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 bond pdb=" C4 YLI E 506 " pdb=" C9 YLI E 506 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 bond pdb=" C4 YLI C 507 " pdb=" C9 YLI C 507 " ideal model delta sigma weight residual 0.000 1.518 -1.518 2.00e-02 2.50e+03 5.76e+03 ... (remaining 33585 not shown) Histogram of bond angle deviations from ideal: 95.53 - 103.24: 235 103.24 - 110.96: 33904 110.96 - 118.67: 11048 118.67 - 126.38: 14592 126.38 - 134.10: 441 Bond angle restraints: 60220 Sorted by residual: angle pdb=" O15 YLI D 507 " pdb=" S14 YLI D 507 " pdb=" O16 YLI D 507 " ideal model delta sigma weight residual 101.63 118.82 -17.19 3.00e+00 1.11e-01 3.28e+01 angle pdb=" O15 YLI C 507 " pdb=" S14 YLI C 507 " pdb=" O16 YLI C 507 " ideal model delta sigma weight residual 101.63 118.79 -17.16 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O15 YLI B 507 " pdb=" S14 YLI B 507 " pdb=" O16 YLI B 507 " ideal model delta sigma weight residual 101.63 118.78 -17.15 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O15 YLI A 507 " pdb=" S14 YLI A 507 " pdb=" O16 YLI A 507 " ideal model delta sigma weight residual 101.63 118.77 -17.14 3.00e+00 1.11e-01 3.27e+01 angle pdb=" O15 YLI E 506 " pdb=" S14 YLI E 506 " pdb=" O16 YLI E 506 " ideal model delta sigma weight residual 101.63 118.77 -17.14 3.00e+00 1.11e-01 3.26e+01 ... (remaining 60215 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.64: 16212 31.64 - 63.29: 528 63.29 - 94.93: 85 94.93 - 126.58: 35 126.58 - 158.22: 10 Dihedral angle restraints: 16870 sinusoidal: 9675 harmonic: 7195 Sorted by residual: dihedral pdb=" CA CYS E 189 " pdb=" C CYS E 189 " pdb=" N CYS E 190 " pdb=" CA CYS E 190 " ideal model delta harmonic sigma weight residual 180.00 -154.59 -25.41 0 5.00e+00 4.00e-02 2.58e+01 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 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA CYS D 189 " pdb=" C CYS D 189 " pdb=" N CYS D 190 " pdb=" CA CYS D 190 " ideal model delta harmonic sigma weight residual -180.00 -154.63 -25.37 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 16867 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2700 0.145 - 0.290: 40 0.290 - 0.435: 5 0.435 - 0.579: 0 0.579 - 0.724: 5 Chirality restraints: 2750 Sorted by residual: chirality pdb=" C6 YLI E 506 " pdb=" C18 YLI E 506 " pdb=" C5 YLI E 506 " pdb=" N7 YLI E 506 " both_signs ideal model delta sigma weight residual False 1.74 2.46 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C6 YLI B 507 " pdb=" C18 YLI B 507 " pdb=" C5 YLI B 507 " pdb=" N7 YLI B 507 " both_signs ideal model delta sigma weight residual False 1.74 2.46 -0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" C6 YLI A 507 " pdb=" C18 YLI A 507 " pdb=" C5 YLI A 507 " pdb=" N7 YLI A 507 " both_signs ideal model delta sigma weight residual False 1.74 2.46 -0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 2747 not shown) Planarity restraints: 4745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.079 2.00e-02 2.50e+03 6.68e-02 5.58e+01 pdb=" C7 NAG C 502 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.106 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 502 " 0.079 2.00e-02 2.50e+03 6.67e-02 5.56e+01 pdb=" C7 NAG B 502 " -0.017 2.00e-02 2.50e+03 pdb=" C8 NAG B 502 " -0.020 2.00e-02 2.50e+03 pdb=" N2 NAG B 502 " -0.106 2.00e-02 2.50e+03 pdb=" O7 NAG B 502 " 0.064 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG D 502 " -0.079 2.00e-02 2.50e+03 6.67e-02 5.56e+01 pdb=" C7 NAG D 502 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG D 502 " 0.020 2.00e-02 2.50e+03 pdb=" N2 NAG D 502 " 0.106 2.00e-02 2.50e+03 pdb=" O7 NAG D 502 " -0.064 2.00e-02 2.50e+03 ... (remaining 4742 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.22: 2299 2.22 - 2.84: 73483 2.84 - 3.46: 89774 3.46 - 4.08: 138727 4.08 - 4.70: 208453 Nonbonded interactions: 512736 Sorted by model distance: nonbonded pdb=" HZ1 LYS B 144 " pdb=" HH TYR B 187 " model vdw 1.606 2.100 nonbonded pdb=" HZ1 LYS C 144 " pdb=" HH TYR C 187 " model vdw 1.606 2.100 nonbonded pdb=" HZ1 LYS A 144 " pdb=" HH TYR A 187 " model vdw 1.607 2.100 nonbonded pdb=" HZ1 LYS E 144 " pdb=" HH TYR E 187 " model vdw 1.607 2.100 nonbonded pdb=" HZ1 LYS D 144 " pdb=" HH TYR D 187 " model vdw 1.607 2.100 ... (remaining 512731 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 113 or resid 115 through \ 478 or resid 501 through 503)) selection = (chain 'B' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478 or resid 501 through 503)) selection = (chain 'C' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478 or resid 501 through 503)) selection = (chain 'D' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478 or resid 501 through 503)) selection = (chain 'E' and (resid 1 through 55 or resid 57 through 113 or resid 115 through \ 478 or resid 501 through 503)) } 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=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.440 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: 0.490 Extract box with map and model: 5.240 Check model and map are aligned: 0.460 Set scattering table: 0.330 Process input model: 128.450 Find NCS groups from input model: 1.980 Set up NCS constraints: 0.330 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: 0.020 Load rotamer database and sin/cos tables:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 153.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 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 : 0.033 1.518 17715 Z= 1.554 Angle : 0.981 17.186 24125 Z= 0.420 Chirality : 0.059 0.724 2750 Planarity : 0.006 0.067 2860 Dihedral : 18.175 158.219 7475 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % 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 (0.17), residues: 1960 helix: -0.37 (0.16), residues: 815 sheet: -0.63 (0.22), residues: 445 loop : -0.14 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 133 HIS 0.004 0.001 HIS E 104 PHE 0.019 0.002 PHE E 99 TYR 0.015 0.002 TYR D 273 ARG 0.012 0.002 ARG C 425 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 230 time to evaluate : 2.858 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8039 (mp) cc_final: 0.7760 (tp) REVERT: B 159 MET cc_start: 0.8546 (ttp) cc_final: 0.8274 (ttp) REVERT: B 446 ARG cc_start: 0.8419 (tpp80) cc_final: 0.8162 (tpp80) REVERT: C 57 MET cc_start: 0.8991 (mtm) cc_final: 0.8737 (mtm) REVERT: C 128 TYR cc_start: 0.8746 (t80) cc_final: 0.8486 (t80) REVERT: C 188 GLU cc_start: 0.6927 (mt-10) cc_final: 0.6470 (mt-10) REVERT: C 210 TYR cc_start: 0.8544 (m-80) cc_final: 0.8255 (m-80) REVERT: D 159 MET cc_start: 0.8491 (ttp) cc_final: 0.8272 (ttp) REVERT: D 188 GLU cc_start: 0.6892 (mt-10) cc_final: 0.6600 (mt-10) REVERT: E 159 MET cc_start: 0.8516 (ttp) cc_final: 0.8297 (ttp) REVERT: E 170 ASN cc_start: 0.7685 (t0) cc_final: 0.7411 (t0) REVERT: E 253 MET cc_start: 0.8912 (ttp) cc_final: 0.8691 (ttp) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 3.2414 time to fit residues: 823.4463 Evaluate side-chains 199 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 2.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 152 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 113 optimal weight: 3.9990 chunk 177 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 17715 Z= 0.285 Angle : 0.773 13.178 24125 Z= 0.373 Chirality : 0.043 0.236 2750 Planarity : 0.005 0.038 2860 Dihedral : 19.758 158.907 3695 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.61 % Allowed : 4.86 % Favored : 94.53 % 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: 0.15 (0.18), residues: 1960 helix: 0.70 (0.17), residues: 815 sheet: -0.62 (0.22), residues: 445 loop : 0.14 (0.24), residues: 700 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 0.019 0.002 PHE A 99 TYR 0.011 0.002 TYR C 273 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 199 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8105 (mp) cc_final: 0.7749 (tp) REVERT: B 159 MET cc_start: 0.8506 (ttp) cc_final: 0.8281 (ttp) REVERT: B 196 ASP cc_start: 0.8493 (p0) cc_final: 0.8154 (p0) REVERT: B 446 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8012 (tpp80) REVERT: C 57 MET cc_start: 0.9001 (mtm) cc_final: 0.8622 (mtm) REVERT: C 210 TYR cc_start: 0.8548 (m-80) cc_final: 0.8226 (m-80) REVERT: E 159 MET cc_start: 0.8492 (ttp) cc_final: 0.8274 (ttp) REVERT: E 170 ASN cc_start: 0.7655 (t0) cc_final: 0.7389 (t0) REVERT: E 196 ASP cc_start: 0.8504 (p0) cc_final: 0.8144 (p0) outliers start: 11 outliers final: 4 residues processed: 202 average time/residue: 3.2771 time to fit residues: 729.9375 Evaluate side-chains 204 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 2.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 12 LYS 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: 3.9990 chunk 147 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 177 optimal weight: 0.9990 chunk 191 optimal weight: 2.9990 chunk 157 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 17715 Z= 0.285 Angle : 0.773 13.178 24125 Z= 0.373 Chirality : 0.043 0.236 2750 Planarity : 0.005 0.038 2860 Dihedral : 19.758 158.907 3695 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.22 % Allowed : 5.59 % Favored : 94.19 % 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: 0.15 (0.18), residues: 1960 helix: 0.70 (0.17), residues: 815 sheet: -0.62 (0.22), residues: 445 loop : 0.14 (0.24), residues: 700 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 0.019 0.002 PHE A 99 TYR 0.011 0.002 TYR C 273 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 200 time to evaluate : 2.603 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8107 (mp) cc_final: 0.7749 (tp) REVERT: B 159 MET cc_start: 0.8504 (ttp) cc_final: 0.8280 (ttp) REVERT: B 196 ASP cc_start: 0.8491 (p0) cc_final: 0.8154 (p0) REVERT: B 446 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8011 (tpp80) REVERT: C 57 MET cc_start: 0.9001 (mtm) cc_final: 0.8621 (mtm) REVERT: C 210 TYR cc_start: 0.8548 (m-80) cc_final: 0.8226 (m-80) REVERT: E 159 MET cc_start: 0.8485 (ttp) cc_final: 0.8274 (ttp) REVERT: E 170 ASN cc_start: 0.7654 (t0) cc_final: 0.7389 (t0) REVERT: E 196 ASP cc_start: 0.8503 (p0) cc_final: 0.8144 (p0) outliers start: 4 outliers final: 4 residues processed: 202 average time/residue: 3.3322 time to fit residues: 740.9241 Evaluate side-chains 200 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 196 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 12 LYS 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: 1.9990 chunk 92 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 84 optimal weight: 0.9990 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 188 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 168 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.133 17715 Z= 0.285 Angle : 0.772 13.178 24125 Z= 0.373 Chirality : 0.043 0.236 2750 Planarity : 0.005 0.038 2860 Dihedral : 19.757 158.907 3695 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 0.22 % Allowed : 5.70 % Favored : 94.08 % 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: 0.15 (0.18), residues: 1960 helix: 0.70 (0.17), residues: 815 sheet: -0.62 (0.22), residues: 445 loop : 0.14 (0.24), residues: 700 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 0.019 0.002 PHE A 99 TYR 0.011 0.002 TYR C 273 ARG 0.002 0.000 ARG A 205 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 196 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8107 (mp) cc_final: 0.7749 (tp) REVERT: B 159 MET cc_start: 0.8504 (ttp) cc_final: 0.8280 (ttp) REVERT: B 196 ASP cc_start: 0.8491 (p0) cc_final: 0.8154 (p0) REVERT: B 446 ARG cc_start: 0.8300 (tpp80) cc_final: 0.8011 (tpp80) REVERT: C 57 MET cc_start: 0.9001 (mtm) cc_final: 0.8621 (mtm) REVERT: C 210 TYR cc_start: 0.8548 (m-80) cc_final: 0.8226 (m-80) REVERT: E 159 MET cc_start: 0.8485 (ttp) cc_final: 0.8274 (ttp) REVERT: E 170 ASN cc_start: 0.7654 (t0) cc_final: 0.7389 (t0) REVERT: E 196 ASP cc_start: 0.8503 (p0) cc_final: 0.8144 (p0) outliers start: 4 outliers final: 4 residues processed: 198 average time/residue: 3.3189 time to fit residues: 724.5606 Evaluate side-chains 200 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 196 time to evaluate : 2.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 12 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 156 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 160 optimal weight: 0.4980 chunk 130 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 96 optimal weight: 0.9980 chunk 169 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17715 Z= 0.254 Angle : 0.747 12.759 24125 Z= 0.361 Chirality : 0.041 0.167 2750 Planarity : 0.005 0.036 2860 Dihedral : 19.645 159.060 3695 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % 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: 0.26 (0.18), residues: 1960 helix: 0.86 (0.17), residues: 815 sheet: -0.61 (0.22), residues: 445 loop : 0.14 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS A 62 PHE 0.019 0.001 PHE A 99 TYR 0.011 0.002 TYR B 210 ARG 0.003 0.000 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 196 time to evaluate : 2.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8115 (mp) cc_final: 0.7756 (tp) REVERT: B 159 MET cc_start: 0.8501 (ttp) cc_final: 0.8281 (ttp) REVERT: B 196 ASP cc_start: 0.8489 (p0) cc_final: 0.8152 (p0) REVERT: B 446 ARG cc_start: 0.8314 (tpp80) cc_final: 0.8027 (tpp80) REVERT: C 57 MET cc_start: 0.9002 (mtm) cc_final: 0.8626 (mtm) REVERT: C 210 TYR cc_start: 0.8549 (m-80) cc_final: 0.8226 (m-80) REVERT: E 159 MET cc_start: 0.8484 (ttp) cc_final: 0.8271 (ttp) REVERT: E 170 ASN cc_start: 0.7650 (t0) cc_final: 0.7383 (t0) REVERT: E 196 ASP cc_start: 0.8503 (p0) cc_final: 0.8144 (p0) outliers start: 3 outliers final: 3 residues processed: 197 average time/residue: 3.3411 time to fit residues: 725.6183 Evaluate side-chains 198 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain E residue 12 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 63 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 188 optimal weight: 6.9990 chunk 156 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 99 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17715 Z= 0.254 Angle : 0.747 12.758 24125 Z= 0.361 Chirality : 0.041 0.167 2750 Planarity : 0.005 0.036 2860 Dihedral : 19.645 159.060 3695 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.17 % Allowed : 5.75 % Favored : 94.08 % 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: 0.26 (0.18), residues: 1960 helix: 0.86 (0.17), residues: 815 sheet: -0.61 (0.22), residues: 445 loop : 0.14 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS A 62 PHE 0.019 0.001 PHE A 99 TYR 0.011 0.002 TYR B 210 ARG 0.003 0.000 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.608 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8115 (mp) cc_final: 0.7756 (tp) REVERT: B 159 MET cc_start: 0.8501 (ttp) cc_final: 0.8281 (ttp) REVERT: B 196 ASP cc_start: 0.8489 (p0) cc_final: 0.8152 (p0) REVERT: B 446 ARG cc_start: 0.8314 (tpp80) cc_final: 0.8027 (tpp80) REVERT: C 57 MET cc_start: 0.9002 (mtm) cc_final: 0.8626 (mtm) REVERT: C 210 TYR cc_start: 0.8549 (m-80) cc_final: 0.8226 (m-80) REVERT: E 159 MET cc_start: 0.8485 (ttp) cc_final: 0.8271 (ttp) REVERT: E 170 ASN cc_start: 0.7650 (t0) cc_final: 0.7383 (t0) REVERT: E 196 ASP cc_start: 0.8503 (p0) cc_final: 0.8144 (p0) outliers start: 3 outliers final: 3 residues processed: 196 average time/residue: 3.4329 time to fit residues: 745.4228 Evaluate side-chains 198 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain E residue 12 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 158 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 187 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 86 optimal weight: 0.0770 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17715 Z= 0.254 Angle : 0.747 12.758 24125 Z= 0.361 Chirality : 0.041 0.167 2750 Planarity : 0.005 0.036 2860 Dihedral : 19.645 159.060 3695 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.17 % Allowed : 5.75 % Favored : 94.08 % 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: 0.26 (0.18), residues: 1960 helix: 0.86 (0.17), residues: 815 sheet: -0.61 (0.22), residues: 445 loop : 0.14 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 307 HIS 0.002 0.001 HIS A 62 PHE 0.019 0.001 PHE A 99 TYR 0.011 0.002 TYR B 210 ARG 0.003 0.000 ARG D 446 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.663 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8115 (mp) cc_final: 0.7756 (tp) REVERT: B 159 MET cc_start: 0.8501 (ttp) cc_final: 0.8281 (ttp) REVERT: B 196 ASP cc_start: 0.8489 (p0) cc_final: 0.8152 (p0) REVERT: B 446 ARG cc_start: 0.8314 (tpp80) cc_final: 0.8027 (tpp80) REVERT: C 57 MET cc_start: 0.9002 (mtm) cc_final: 0.8626 (mtm) REVERT: C 210 TYR cc_start: 0.8549 (m-80) cc_final: 0.8226 (m-80) REVERT: E 159 MET cc_start: 0.8485 (ttp) cc_final: 0.8271 (ttp) REVERT: E 170 ASN cc_start: 0.7650 (t0) cc_final: 0.7383 (t0) REVERT: E 196 ASP cc_start: 0.8503 (p0) cc_final: 0.8144 (p0) outliers start: 3 outliers final: 3 residues processed: 196 average time/residue: 3.3109 time to fit residues: 714.6041 Evaluate side-chains 198 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 2.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain E residue 12 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 116 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 119 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 147 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 17715 Z= 0.296 Angle : 0.721 11.542 24125 Z= 0.353 Chirality : 0.042 0.198 2750 Planarity : 0.005 0.041 2860 Dihedral : 19.142 158.492 3695 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.45 % Allowed : 5.59 % Favored : 93.97 % 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: 0.59 (0.18), residues: 1960 helix: 1.29 (0.17), residues: 815 sheet: -0.56 (0.22), residues: 445 loop : 0.18 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 307 HIS 0.003 0.001 HIS D 140 PHE 0.019 0.002 PHE A 99 TYR 0.012 0.002 TYR B 210 ARG 0.008 0.001 ARG D 4 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 195 time to evaluate : 2.641 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8127 (mp) cc_final: 0.7733 (tp) REVERT: B 159 MET cc_start: 0.8506 (ttp) cc_final: 0.8297 (ttp) REVERT: B 196 ASP cc_start: 0.8473 (p0) cc_final: 0.8132 (p0) REVERT: B 446 ARG cc_start: 0.8317 (tpp80) cc_final: 0.7973 (tpp80) REVERT: C 57 MET cc_start: 0.9024 (mtm) cc_final: 0.8644 (mtm) REVERT: C 210 TYR cc_start: 0.8544 (m-80) cc_final: 0.8223 (m-80) REVERT: E 170 ASN cc_start: 0.7672 (t0) cc_final: 0.7396 (t0) REVERT: E 196 ASP cc_start: 0.8501 (p0) cc_final: 0.8173 (p0) outliers start: 8 outliers final: 4 residues processed: 197 average time/residue: 3.3128 time to fit residues: 719.3662 Evaluate side-chains 199 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 195 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 12 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 180 optimal weight: 3.9990 chunk 164 optimal weight: 0.6980 chunk 175 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 137 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 158 optimal weight: 0.9990 chunk 165 optimal weight: 1.9990 chunk 174 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17715 Z= 0.231 Angle : 0.672 9.435 24125 Z= 0.333 Chirality : 0.042 0.210 2750 Planarity : 0.005 0.043 2860 Dihedral : 18.825 158.027 3695 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.28 % Allowed : 5.70 % Favored : 94.02 % 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: 0.69 (0.18), residues: 1960 helix: 1.43 (0.17), residues: 815 sheet: -0.53 (0.23), residues: 440 loop : 0.17 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 307 HIS 0.003 0.001 HIS C 140 PHE 0.018 0.002 PHE A 99 TYR 0.011 0.002 TYR C 210 ARG 0.004 0.000 ARG E 446 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 199 time to evaluate : 2.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8125 (mp) cc_final: 0.7720 (tp) REVERT: B 159 MET cc_start: 0.8500 (ttp) cc_final: 0.8295 (ttp) REVERT: B 196 ASP cc_start: 0.8481 (p0) cc_final: 0.8146 (p0) REVERT: B 446 ARG cc_start: 0.8308 (tpp80) cc_final: 0.7970 (tpp80) REVERT: C 57 MET cc_start: 0.9025 (mtm) cc_final: 0.8642 (mtm) REVERT: C 210 TYR cc_start: 0.8540 (m-80) cc_final: 0.8220 (m-80) REVERT: E 170 ASN cc_start: 0.7655 (t0) cc_final: 0.7383 (t0) REVERT: E 196 ASP cc_start: 0.8496 (p0) cc_final: 0.8143 (p0) outliers start: 5 outliers final: 5 residues processed: 200 average time/residue: 3.3710 time to fit residues: 742.3909 Evaluate side-chains 203 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 198 time to evaluate : 2.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 311 ILE Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain E residue 12 LYS 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: 3.9990 chunk 87 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 178 optimal weight: 0.7980 chunk 154 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 119 optimal weight: 0.8980 chunk 94 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.0996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 17715 Z= 0.204 Angle : 0.649 10.618 24125 Z= 0.320 Chirality : 0.042 0.454 2750 Planarity : 0.004 0.046 2860 Dihedral : 18.210 156.913 3695 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.34 % Allowed : 5.70 % Favored : 93.97 % 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: 0.86 (0.19), residues: 1960 helix: 1.63 (0.17), residues: 815 sheet: -0.52 (0.23), residues: 440 loop : 0.22 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 307 HIS 0.003 0.001 HIS C 140 PHE 0.015 0.001 PHE A 99 TYR 0.011 0.001 TYR C 210 ARG 0.005 0.001 ARG E 446 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3920 Ramachandran restraints generated. 1960 Oldfield, 0 Emsley, 1960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 198 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 247 LEU cc_start: 0.8128 (mp) cc_final: 0.7699 (tp) REVERT: B 159 MET cc_start: 0.8488 (ttp) cc_final: 0.8287 (ttp) REVERT: B 196 ASP cc_start: 0.8472 (p0) cc_final: 0.8143 (p0) REVERT: B 446 ARG cc_start: 0.8292 (tpp80) cc_final: 0.8033 (tpp80) REVERT: C 57 MET cc_start: 0.9022 (mtm) cc_final: 0.8632 (mtm) REVERT: C 210 TYR cc_start: 0.8523 (m-80) cc_final: 0.8205 (m-80) REVERT: E 170 ASN cc_start: 0.7629 (t0) cc_final: 0.7374 (t0) outliers start: 6 outliers final: 6 residues processed: 200 average time/residue: 3.2886 time to fit residues: 726.1936 Evaluate side-chains 203 residues out of total 1770 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 197 time to evaluate : 2.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 461 ILE Chi-restraints excluded: chain D residue 161 GLU Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 12 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 1.9990 chunk 47 optimal weight: 0.1980 chunk 142 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 114 HIS B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.129062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.097359 restraints weight = 51148.449| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.55 r_work: 0.2865 rms_B_bonded: 1.51 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17715 Z= 0.203 Angle : 0.637 9.090 24125 Z= 0.313 Chirality : 0.043 0.526 2750 Planarity : 0.004 0.047 2860 Dihedral : 17.985 155.965 3695 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 0.28 % Allowed : 5.92 % Favored : 93.80 % 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: 0.89 (0.19), residues: 1960 helix: 1.67 (0.17), residues: 815 sheet: -0.51 (0.23), residues: 440 loop : 0.23 (0.24), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 307 HIS 0.002 0.001 HIS C 140 PHE 0.015 0.001 PHE A 99 TYR 0.011 0.001 TYR C 210 ARG 0.006 0.000 ARG D 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12273.21 seconds wall clock time: 218 minutes 6.33 seconds (13086.33 seconds total)