Starting phenix.real_space_refine on Mon Mar 18 19:28:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/03_2024/7kvc_23046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/03_2024/7kvc_23046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/03_2024/7kvc_23046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/03_2024/7kvc_23046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/03_2024/7kvc_23046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/03_2024/7kvc_23046.pdb" } resolution = 4.7 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= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 14120 2.51 5 N 3590 2.21 5 O 4170 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 207": "NH1" <-> "NH2" Residue "A ARG 272": "NH1" <-> "NH2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 312": "NH1" <-> "NH2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B ARG 272": "NH1" <-> "NH2" Residue "B TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 312": "NH1" <-> "NH2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 207": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 312": "NH1" <-> "NH2" Residue "C PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 207": "NH1" <-> "NH2" Residue "D ARG 272": "NH1" <-> "NH2" Residue "D TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 312": "NH1" <-> "NH2" Residue "D PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 174": "OE1" <-> "OE2" Residue "E PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 207": "NH1" <-> "NH2" Residue "E ARG 272": "NH1" <-> "NH2" Residue "E TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 312": "NH1" <-> "NH2" Residue "E PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 174": "OE1" <-> "OE2" Residue "F PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 207": "NH1" <-> "NH2" Residue "F ARG 272": "NH1" <-> "NH2" Residue "F TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 312": "NH1" <-> "NH2" Residue "F PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 174": "OE1" <-> "OE2" Residue "G PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 207": "NH1" <-> "NH2" Residue "G ARG 272": "NH1" <-> "NH2" Residue "G TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 312": "NH1" <-> "NH2" Residue "G PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 174": "OE1" <-> "OE2" Residue "H PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 207": "NH1" <-> "NH2" Residue "H ARG 272": "NH1" <-> "NH2" Residue "H TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 312": "NH1" <-> "NH2" Residue "H PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 174": "OE1" <-> "OE2" Residue "I PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 207": "NH1" <-> "NH2" Residue "I ARG 272": "NH1" <-> "NH2" Residue "I TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 312": "NH1" <-> "NH2" Residue "I PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 174": "OE1" <-> "OE2" Residue "J PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 207": "NH1" <-> "NH2" Residue "J ARG 272": "NH1" <-> "NH2" Residue "J TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 312": "NH1" <-> "NH2" Residue "J PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 21920 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "B" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "C" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "D" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "E" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "F" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "G" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "H" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "I" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Chain: "J" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 257} Chain breaks: 6 Time building chain proxies: 11.50, per 1000 atoms: 0.52 Number of scatterers: 21920 At special positions: 0 Unit cell: (136.85, 138.55, 99.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 4170 8.00 N 3590 7.00 C 14120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.75 Conformation dependent library (CDL) restraints added in 3.6 seconds 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5060 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 30 sheets defined 42.9% alpha, 12.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 52 through 62 Processing helix chain 'A' and resid 64 through 68 Processing helix chain 'A' and resid 80 through 101 removed outlier: 3.948A pdb=" N ILE A 99 " --> pdb=" O ASN A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 201 Processing helix chain 'A' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG A 207 " --> pdb=" O SER A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 213 No H-bonds generated for 'chain 'A' and resid 211 through 213' Processing helix chain 'A' and resid 214 through 227 Processing helix chain 'A' and resid 239 through 247 removed outlier: 3.748A pdb=" N PHE A 247 " --> pdb=" O GLN A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 251 through 259 Processing helix chain 'A' and resid 271 through 276 removed outlier: 4.104A pdb=" N ASP A 276 " --> pdb=" O ARG A 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 62 Processing helix chain 'B' and resid 64 through 68 Processing helix chain 'B' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 201 Processing helix chain 'B' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG B 207 " --> pdb=" O SER B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 213 No H-bonds generated for 'chain 'B' and resid 211 through 213' Processing helix chain 'B' and resid 214 through 227 Processing helix chain 'B' and resid 239 through 247 removed outlier: 3.748A pdb=" N PHE B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 259 Processing helix chain 'B' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP B 276 " --> pdb=" O ARG B 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 62 Processing helix chain 'C' and resid 64 through 68 Processing helix chain 'C' and resid 80 through 101 removed outlier: 3.950A pdb=" N ILE C 99 " --> pdb=" O ASN C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 201 Processing helix chain 'C' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG C 207 " --> pdb=" O SER C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 211 through 213 No H-bonds generated for 'chain 'C' and resid 211 through 213' Processing helix chain 'C' and resid 214 through 227 Processing helix chain 'C' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE C 247 " --> pdb=" O GLN C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 259 Processing helix chain 'C' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP C 276 " --> pdb=" O ARG C 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 62 Processing helix chain 'D' and resid 64 through 68 Processing helix chain 'D' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE D 99 " --> pdb=" O ASN D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 201 Processing helix chain 'D' and resid 203 through 208 removed outlier: 4.319A pdb=" N ARG D 207 " --> pdb=" O SER D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 211 through 213 No H-bonds generated for 'chain 'D' and resid 211 through 213' Processing helix chain 'D' and resid 214 through 227 Processing helix chain 'D' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE D 247 " --> pdb=" O GLN D 243 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 259 Processing helix chain 'D' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP D 276 " --> pdb=" O ARG D 272 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 62 Processing helix chain 'E' and resid 64 through 68 Processing helix chain 'E' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE E 99 " --> pdb=" O ASN E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 201 Processing helix chain 'E' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG E 207 " --> pdb=" O SER E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 211 through 213 No H-bonds generated for 'chain 'E' and resid 211 through 213' Processing helix chain 'E' and resid 214 through 227 Processing helix chain 'E' and resid 239 through 247 removed outlier: 3.748A pdb=" N PHE E 247 " --> pdb=" O GLN E 243 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 259 Processing helix chain 'E' and resid 271 through 276 removed outlier: 4.104A pdb=" N ASP E 276 " --> pdb=" O ARG E 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 62 Processing helix chain 'F' and resid 64 through 68 Processing helix chain 'F' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE F 99 " --> pdb=" O ASN F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 201 Processing helix chain 'F' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG F 207 " --> pdb=" O SER F 204 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 213 No H-bonds generated for 'chain 'F' and resid 211 through 213' Processing helix chain 'F' and resid 214 through 227 Processing helix chain 'F' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE F 247 " --> pdb=" O GLN F 243 " (cutoff:3.500A) Processing helix chain 'F' and resid 251 through 259 Processing helix chain 'F' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP F 276 " --> pdb=" O ARG F 272 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 62 Processing helix chain 'G' and resid 64 through 68 Processing helix chain 'G' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE G 99 " --> pdb=" O ASN G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 201 Processing helix chain 'G' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG G 207 " --> pdb=" O SER G 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 213 No H-bonds generated for 'chain 'G' and resid 211 through 213' Processing helix chain 'G' and resid 214 through 227 Processing helix chain 'G' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE G 247 " --> pdb=" O GLN G 243 " (cutoff:3.500A) Processing helix chain 'G' and resid 251 through 259 Processing helix chain 'G' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP G 276 " --> pdb=" O ARG G 272 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 62 Processing helix chain 'H' and resid 64 through 68 Processing helix chain 'H' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE H 99 " --> pdb=" O ASN H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 201 Processing helix chain 'H' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG H 207 " --> pdb=" O SER H 204 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 213 No H-bonds generated for 'chain 'H' and resid 211 through 213' Processing helix chain 'H' and resid 214 through 227 Processing helix chain 'H' and resid 239 through 247 removed outlier: 3.748A pdb=" N PHE H 247 " --> pdb=" O GLN H 243 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 259 Processing helix chain 'H' and resid 271 through 276 removed outlier: 4.104A pdb=" N ASP H 276 " --> pdb=" O ARG H 272 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 62 Processing helix chain 'I' and resid 64 through 68 Processing helix chain 'I' and resid 80 through 101 removed outlier: 3.950A pdb=" N ILE I 99 " --> pdb=" O ASN I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 201 Processing helix chain 'I' and resid 203 through 208 removed outlier: 4.318A pdb=" N ARG I 207 " --> pdb=" O SER I 204 " (cutoff:3.500A) Processing helix chain 'I' and resid 211 through 213 No H-bonds generated for 'chain 'I' and resid 211 through 213' Processing helix chain 'I' and resid 214 through 227 Processing helix chain 'I' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE I 247 " --> pdb=" O GLN I 243 " (cutoff:3.500A) Processing helix chain 'I' and resid 251 through 259 Processing helix chain 'I' and resid 271 through 276 removed outlier: 4.103A pdb=" N ASP I 276 " --> pdb=" O ARG I 272 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 62 Processing helix chain 'J' and resid 64 through 68 Processing helix chain 'J' and resid 80 through 101 removed outlier: 3.949A pdb=" N ILE J 99 " --> pdb=" O ASN J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 201 Processing helix chain 'J' and resid 203 through 208 removed outlier: 4.319A pdb=" N ARG J 207 " --> pdb=" O SER J 204 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 213 No H-bonds generated for 'chain 'J' and resid 211 through 213' Processing helix chain 'J' and resid 214 through 227 Processing helix chain 'J' and resid 239 through 247 removed outlier: 3.747A pdb=" N PHE J 247 " --> pdb=" O GLN J 243 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 259 Processing helix chain 'J' and resid 271 through 276 removed outlier: 4.104A pdb=" N ASP J 276 " --> pdb=" O ARG J 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 17 Processing sheet with id=AA2, first strand: chain 'A' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU A 116 " --> pdb=" O LYS A 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS A 309 " --> pdb=" O LEU A 116 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER A 302 " --> pdb=" O GLY A 298 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 13 through 17 Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU B 116 " --> pdb=" O LYS B 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS B 309 " --> pdb=" O LEU B 116 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 279 through 285 removed outlier: 3.504A pdb=" N SER B 302 " --> pdb=" O GLY B 298 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 13 through 17 Processing sheet with id=AA8, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU C 116 " --> pdb=" O LYS C 309 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS C 309 " --> pdb=" O LEU C 116 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 279 through 285 removed outlier: 3.504A pdb=" N SER C 302 " --> pdb=" O GLY C 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 13 through 17 Processing sheet with id=AB2, first strand: chain 'D' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU D 116 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS D 309 " --> pdb=" O LEU D 116 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER D 302 " --> pdb=" O GLY D 298 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 13 through 17 Processing sheet with id=AB5, first strand: chain 'E' and resid 156 through 159 removed outlier: 4.128A pdb=" N LEU E 116 " --> pdb=" O LYS E 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS E 309 " --> pdb=" O LEU E 116 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER E 302 " --> pdb=" O GLY E 298 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 13 through 17 Processing sheet with id=AB8, first strand: chain 'F' and resid 156 through 159 removed outlier: 4.128A pdb=" N LEU F 116 " --> pdb=" O LYS F 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS F 309 " --> pdb=" O LEU F 116 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER F 302 " --> pdb=" O GLY F 298 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 13 through 17 Processing sheet with id=AC2, first strand: chain 'G' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU G 116 " --> pdb=" O LYS G 309 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS G 309 " --> pdb=" O LEU G 116 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 279 through 285 removed outlier: 3.504A pdb=" N SER G 302 " --> pdb=" O GLY G 298 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 13 through 17 Processing sheet with id=AC5, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.128A pdb=" N LEU H 116 " --> pdb=" O LYS H 309 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS H 309 " --> pdb=" O LEU H 116 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER H 302 " --> pdb=" O GLY H 298 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 13 through 17 Processing sheet with id=AC8, first strand: chain 'I' and resid 156 through 159 removed outlier: 4.128A pdb=" N LEU I 116 " --> pdb=" O LYS I 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS I 309 " --> pdb=" O LEU I 116 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 279 through 285 removed outlier: 3.504A pdb=" N SER I 302 " --> pdb=" O GLY I 298 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 13 through 17 Processing sheet with id=AD2, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.127A pdb=" N LEU J 116 " --> pdb=" O LYS J 309 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS J 309 " --> pdb=" O LEU J 116 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 279 through 285 removed outlier: 3.503A pdb=" N SER J 302 " --> pdb=" O GLY J 298 " (cutoff:3.500A) 960 hydrogen bonds defined for protein. 2610 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: 5.93 Time building geometry restraints manager: 9.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6996 1.34 - 1.46: 4253 1.46 - 1.57: 10971 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 22290 Sorted by residual: bond pdb=" C ASP C 329 " pdb=" N PHE C 330 " ideal model delta sigma weight residual 1.332 1.310 0.023 1.40e-02 5.10e+03 2.60e+00 bond pdb=" C ASP G 329 " pdb=" N PHE G 330 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.57e+00 bond pdb=" C ASP D 329 " pdb=" N PHE D 330 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.51e+00 bond pdb=" C ASP J 329 " pdb=" N PHE J 330 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.50e+00 bond pdb=" C ASP B 329 " pdb=" N PHE B 330 " ideal model delta sigma weight residual 1.332 1.310 0.022 1.40e-02 5.10e+03 2.45e+00 ... (remaining 22285 not shown) Histogram of bond angle deviations from ideal: 100.08 - 106.35: 373 106.35 - 112.62: 11349 112.62 - 118.90: 6277 118.90 - 125.17: 11861 125.17 - 131.44: 160 Bond angle restraints: 30020 Sorted by residual: angle pdb=" N GLU A 94 " pdb=" CA GLU A 94 " pdb=" CB GLU A 94 " ideal model delta sigma weight residual 110.16 116.23 -6.07 1.48e+00 4.57e-01 1.68e+01 angle pdb=" N GLU H 94 " pdb=" CA GLU H 94 " pdb=" CB GLU H 94 " ideal model delta sigma weight residual 110.16 116.22 -6.06 1.48e+00 4.57e-01 1.68e+01 angle pdb=" N GLU G 94 " pdb=" CA GLU G 94 " pdb=" CB GLU G 94 " ideal model delta sigma weight residual 110.16 116.21 -6.05 1.48e+00 4.57e-01 1.67e+01 angle pdb=" N GLU I 94 " pdb=" CA GLU I 94 " pdb=" CB GLU I 94 " ideal model delta sigma weight residual 110.16 116.20 -6.04 1.48e+00 4.57e-01 1.66e+01 angle pdb=" N GLU F 94 " pdb=" CA GLU F 94 " pdb=" CB GLU F 94 " ideal model delta sigma weight residual 110.16 116.20 -6.04 1.48e+00 4.57e-01 1.66e+01 ... (remaining 30015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.05: 11842 17.05 - 34.11: 1398 34.11 - 51.16: 180 51.16 - 68.22: 30 68.22 - 85.27: 10 Dihedral angle restraints: 13460 sinusoidal: 5650 harmonic: 7810 Sorted by residual: dihedral pdb=" CA ASP B 50 " pdb=" C ASP B 50 " pdb=" N GLY B 51 " pdb=" CA GLY B 51 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA ASP G 50 " pdb=" C ASP G 50 " pdb=" N GLY G 51 " pdb=" CA GLY G 51 " ideal model delta harmonic sigma weight residual 180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.15e+01 dihedral pdb=" CA GLU F 271 " pdb=" C GLU F 271 " pdb=" N ARG F 272 " pdb=" CA ARG F 272 " ideal model delta harmonic sigma weight residual 180.00 -156.84 -23.16 0 5.00e+00 4.00e-02 2.14e+01 ... (remaining 13457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 2198 0.038 - 0.076: 795 0.076 - 0.114: 260 0.114 - 0.152: 137 0.152 - 0.190: 10 Chirality restraints: 3400 Sorted by residual: chirality pdb=" CG LEU F 333 " pdb=" CB LEU F 333 " pdb=" CD1 LEU F 333 " pdb=" CD2 LEU F 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CG LEU J 333 " pdb=" CB LEU J 333 " pdb=" CD1 LEU J 333 " pdb=" CD2 LEU J 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.96e-01 chirality pdb=" CG LEU D 333 " pdb=" CB LEU D 333 " pdb=" CD1 LEU D 333 " pdb=" CD2 LEU D 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.96e-01 ... (remaining 3397 not shown) Planarity restraints: 3800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR D 250 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO D 251 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO D 251 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 251 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR C 250 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO C 251 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 251 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 251 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 250 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 251 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 251 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 251 " 0.026 5.00e-02 4.00e+02 ... (remaining 3797 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 4649 2.76 - 3.29: 25142 3.29 - 3.83: 39098 3.83 - 4.36: 43860 4.36 - 4.90: 66715 Nonbonded interactions: 179464 Sorted by model distance: nonbonded pdb=" NE ARG I 215 " pdb=" O ALA I 245 " model vdw 2.224 2.520 nonbonded pdb=" NE ARG C 215 " pdb=" O ALA C 245 " model vdw 2.224 2.520 nonbonded pdb=" NE ARG A 215 " pdb=" O ALA A 245 " model vdw 2.224 2.520 nonbonded pdb=" NE ARG F 215 " pdb=" O ALA F 245 " model vdw 2.224 2.520 nonbonded pdb=" NE ARG G 215 " pdb=" O ALA G 245 " model vdw 2.224 2.520 ... (remaining 179459 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.760 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: 0.010 Extract box with map and model: 4.490 Check model and map are aligned: 0.310 Set scattering table: 0.200 Process input model: 54.770 Find NCS groups from input model: 1.430 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 65.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 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 : 0.005 0.038 22290 Z= 0.305 Angle : 0.836 6.069 30020 Z= 0.460 Chirality : 0.049 0.190 3400 Planarity : 0.005 0.047 3800 Dihedral : 13.910 85.271 8400 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 33.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -2.46 (0.16), residues: 2520 helix: -0.42 (0.17), residues: 880 sheet: -1.75 (0.24), residues: 420 loop : -2.54 (0.17), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 197 PHE 0.021 0.002 PHE G 330 TYR 0.017 0.002 TYR E 305 ARG 0.007 0.001 ARG H 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5040 Ramachandran restraints generated. 2520 Oldfield, 0 Emsley, 2520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.268 Fit side-chains revert: symmetry clash REVERT: A 85 PHE cc_start: 0.9433 (t80) cc_final: 0.9163 (t80) REVERT: A 198 LEU cc_start: 0.9390 (mt) cc_final: 0.9130 (mt) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0827 time to fit residues: 4.3794 Evaluate side-chains 37 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 219 optimal weight: 6.9990 chunk 197 optimal weight: 0.9990 chunk 109 optimal weight: 6.9990 chunk 67 optimal weight: 0.1980 chunk 132 optimal weight: 8.9990 chunk 105 optimal weight: 8.9990 chunk 203 optimal weight: 20.0000 chunk 78 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 236 optimal weight: 5.9990 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22290 Z= 0.217 Angle : 0.676 5.101 30020 Z= 0.360 Chirality : 0.042 0.126 3400 Planarity : 0.005 0.054 3800 Dihedral : 5.697 21.898 2900 Min Nonbonded Distance : 1.738 Molprobity Statistics. All-atom Clashscore : 25.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 0.40 % Allowed : 8.84 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.73 (0.16), residues: 2520 helix: 0.37 (0.17), residues: 880 sheet: -1.00 (0.26), residues: 350 loop : -2.37 (0.15), residues: 1290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 197 PHE 0.020 0.002 PHE G 226 TYR 0.035 0.002 TYR B 305 ARG 0.005 0.000 ARG C 215 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 43 time to evaluate : 0.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8643 (mmmm) cc_final: 0.8346 (mmmm) REVERT: E 85 PHE cc_start: 0.9271 (t80) cc_final: 0.9044 (t80) REVERT: E 198 LEU cc_start: 0.9431 (mt) cc_final: 0.9134 (mt) REVERT: E 250 TYR cc_start: 0.8212 (t80) cc_final: 0.7919 (t80) outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.0981 time to fit residues: 5.4963 Evaluate side-chains 43 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 131 optimal weight: 0.1980 chunk 73 optimal weight: 7.9990 chunk 196 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 236 optimal weight: 7.9990 chunk 255 optimal weight: 10.0000 chunk 210 optimal weight: 4.9990 chunk 234 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 189 optimal weight: 30.0000 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22290 Z= 0.157 Angle : 0.643 5.644 30020 Z= 0.329 Chirality : 0.042 0.112 3400 Planarity : 0.004 0.046 3800 Dihedral : 4.768 20.016 2900 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -1.13 (0.16), residues: 2520 helix: 0.96 (0.17), residues: 890 sheet: -0.86 (0.27), residues: 350 loop : -2.04 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 197 PHE 0.015 0.001 PHE C 226 TYR 0.011 0.001 TYR E 214 ARG 0.003 0.000 ARG H 215 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8635 (mmmm) cc_final: 0.8314 (mmmm) REVERT: E 85 PHE cc_start: 0.9231 (t80) cc_final: 0.9031 (t80) REVERT: E 198 LEU cc_start: 0.9435 (mt) cc_final: 0.9185 (mt) REVERT: E 222 ILE cc_start: 0.8899 (tp) cc_final: 0.8630 (tp) REVERT: E 250 TYR cc_start: 0.8174 (t80) cc_final: 0.7693 (t80) REVERT: E 295 LEU cc_start: 0.9169 (mm) cc_final: 0.8822 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1048 time to fit residues: 6.7986 Evaluate side-chains 45 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 233 optimal weight: 3.9990 chunk 177 optimal weight: 30.0000 chunk 122 optimal weight: 6.9990 chunk 26 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 158 optimal weight: 5.9990 chunk 237 optimal weight: 0.0870 chunk 251 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 224 optimal weight: 8.9990 chunk 67 optimal weight: 0.0870 overall best weight: 2.4342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 ASN ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22290 Z= 0.162 Angle : 0.616 5.696 30020 Z= 0.320 Chirality : 0.042 0.109 3400 Planarity : 0.004 0.044 3800 Dihedral : 4.594 18.773 2900 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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 (0.16), residues: 2520 helix: 1.09 (0.17), residues: 890 sheet: -1.10 (0.25), residues: 400 loop : -1.77 (0.16), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 197 PHE 0.024 0.002 PHE F 121 TYR 0.008 0.001 TYR H 214 ARG 0.003 0.000 ARG I 215 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 49 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8635 (mmmm) cc_final: 0.8318 (mmmm) REVERT: E 52 ILE cc_start: 0.9170 (mm) cc_final: 0.8856 (mm) REVERT: E 85 PHE cc_start: 0.9174 (t80) cc_final: 0.8778 (t80) REVERT: E 250 TYR cc_start: 0.8249 (t80) cc_final: 0.7798 (t80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0886 time to fit residues: 5.6259 Evaluate side-chains 40 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 209 optimal weight: 5.9990 chunk 142 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 187 optimal weight: 20.0000 chunk 103 optimal weight: 0.5980 chunk 214 optimal weight: 7.9990 chunk 173 optimal weight: 0.5980 chunk 0 optimal weight: 20.0000 chunk 128 optimal weight: 0.0020 chunk 225 optimal weight: 0.9990 chunk 63 optimal weight: 0.0470 overall best weight: 0.4488 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 22290 Z= 0.144 Angle : 0.616 6.693 30020 Z= 0.306 Chirality : 0.041 0.118 3400 Planarity : 0.004 0.042 3800 Dihedral : 4.207 16.531 2900 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.40 % Allowed : 3.21 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.33 (0.17), residues: 2520 helix: 1.68 (0.18), residues: 890 sheet: -0.52 (0.27), residues: 400 loop : -1.60 (0.17), residues: 1230 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 197 PHE 0.006 0.001 PHE C 330 TYR 0.025 0.001 TYR C 214 ARG 0.002 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8614 (mmmm) cc_final: 0.8284 (mmmm) REVERT: E 85 PHE cc_start: 0.9154 (t80) cc_final: 0.8751 (t80) REVERT: E 198 LEU cc_start: 0.9412 (mt) cc_final: 0.9206 (mt) REVERT: E 250 TYR cc_start: 0.8233 (t80) cc_final: 0.7867 (t80) REVERT: E 258 GLN cc_start: 0.8810 (pm20) cc_final: 0.8577 (mm110) outliers start: 1 outliers final: 0 residues processed: 55 average time/residue: 0.1068 time to fit residues: 7.2961 Evaluate side-chains 46 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 84 optimal weight: 8.9990 chunk 226 optimal weight: 3.9990 chunk 49 optimal weight: 0.0670 chunk 147 optimal weight: 6.9990 chunk 62 optimal weight: 10.0000 chunk 251 optimal weight: 0.3980 chunk 208 optimal weight: 20.0000 chunk 116 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 132 optimal weight: 8.9990 overall best weight: 3.4924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 90 ASN ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 22290 Z= 0.180 Angle : 0.617 5.586 30020 Z= 0.325 Chirality : 0.041 0.112 3400 Planarity : 0.004 0.046 3800 Dihedral : 4.379 16.494 2900 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.42 (0.17), residues: 2520 helix: 1.39 (0.18), residues: 890 sheet: 0.14 (0.30), residues: 350 loop : -1.68 (0.17), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 77 PHE 0.027 0.002 PHE C 121 TYR 0.009 0.001 TYR J 224 ARG 0.003 0.000 ARG G 215 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8289 (mmmm) REVERT: E 50 ASP cc_start: 0.8746 (p0) cc_final: 0.8465 (p0) REVERT: E 52 ILE cc_start: 0.9263 (mm) cc_final: 0.8997 (mm) REVERT: E 85 PHE cc_start: 0.9114 (t80) cc_final: 0.8679 (t80) REVERT: E 250 TYR cc_start: 0.8401 (t80) cc_final: 0.7470 (t80) REVERT: E 254 LEU cc_start: 0.9395 (mm) cc_final: 0.8993 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0857 time to fit residues: 5.7715 Evaluate side-chains 42 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 242 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 143 optimal weight: 6.9990 chunk 183 optimal weight: 6.9990 chunk 142 optimal weight: 3.9990 chunk 211 optimal weight: 0.9980 chunk 140 optimal weight: 20.0000 chunk 250 optimal weight: 5.9990 chunk 156 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 115 optimal weight: 0.0870 overall best weight: 3.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 258 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 22290 Z= 0.178 Angle : 0.612 5.767 30020 Z= 0.321 Chirality : 0.041 0.115 3400 Planarity : 0.004 0.042 3800 Dihedral : 4.381 16.082 2900 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 17.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.41 (0.17), residues: 2520 helix: 1.39 (0.17), residues: 890 sheet: 0.23 (0.30), residues: 350 loop : -1.72 (0.16), residues: 1280 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 197 PHE 0.009 0.001 PHE E 257 TYR 0.013 0.001 TYR H 214 ARG 0.003 0.000 ARG J 215 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8730 (mmmm) cc_final: 0.8274 (mmmm) REVERT: E 50 ASP cc_start: 0.8780 (p0) cc_final: 0.8334 (p0) REVERT: E 52 ILE cc_start: 0.9272 (mm) cc_final: 0.8925 (mm) REVERT: E 85 PHE cc_start: 0.9043 (t80) cc_final: 0.8610 (t80) REVERT: E 250 TYR cc_start: 0.8269 (t80) cc_final: 0.7748 (t80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1357 time to fit residues: 8.6079 Evaluate side-chains 42 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 155 optimal weight: 8.9990 chunk 100 optimal weight: 0.9990 chunk 149 optimal weight: 5.9990 chunk 75 optimal weight: 0.0980 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 159 optimal weight: 0.7980 chunk 170 optimal weight: 0.9980 chunk 123 optimal weight: 0.0370 chunk 23 optimal weight: 0.0470 chunk 196 optimal weight: 3.9990 overall best weight: 0.3956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.3702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22290 Z= 0.153 Angle : 0.641 6.908 30020 Z= 0.315 Chirality : 0.042 0.127 3400 Planarity : 0.004 0.037 3800 Dihedral : 4.195 17.882 2900 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: -0.01 (0.17), residues: 2520 helix: 1.60 (0.17), residues: 900 sheet: 0.18 (0.30), residues: 370 loop : -1.32 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 197 PHE 0.029 0.002 PHE H 121 TYR 0.011 0.001 TYR I 250 ARG 0.001 0.000 ARG B 215 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8664 (mmmm) cc_final: 0.8212 (mmmm) REVERT: E 50 ASP cc_start: 0.8657 (p0) cc_final: 0.8031 (t70) REVERT: E 85 PHE cc_start: 0.9040 (t80) cc_final: 0.8635 (t80) REVERT: E 198 LEU cc_start: 0.9434 (mt) cc_final: 0.9187 (mt) REVERT: E 250 TYR cc_start: 0.8099 (t80) cc_final: 0.7657 (t80) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1024 time to fit residues: 7.1543 Evaluate side-chains 46 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 227 optimal weight: 0.0470 chunk 240 optimal weight: 2.9990 chunk 219 optimal weight: 8.9990 chunk 233 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 101 optimal weight: 0.2980 chunk 183 optimal weight: 7.9990 chunk 71 optimal weight: 0.3980 chunk 211 optimal weight: 0.0980 chunk 220 optimal weight: 6.9990 chunk 232 optimal weight: 20.0000 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 22290 Z= 0.150 Angle : 0.631 6.866 30020 Z= 0.315 Chirality : 0.042 0.146 3400 Planarity : 0.003 0.035 3800 Dihedral : 4.165 17.360 2900 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.06 (0.17), residues: 2520 helix: 1.56 (0.17), residues: 900 sheet: 0.50 (0.31), residues: 370 loop : -1.29 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 197 PHE 0.008 0.001 PHE C 279 TYR 0.009 0.001 TYR A 214 ARG 0.002 0.000 ARG F 215 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.291 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8680 (mmmm) cc_final: 0.8222 (mmmm) REVERT: E 50 ASP cc_start: 0.8645 (p0) cc_final: 0.8085 (t70) REVERT: E 85 PHE cc_start: 0.9028 (t80) cc_final: 0.8625 (t80) REVERT: E 198 LEU cc_start: 0.9447 (mt) cc_final: 0.9209 (mt) REVERT: E 250 TYR cc_start: 0.8155 (t80) cc_final: 0.7545 (t80) REVERT: E 254 LEU cc_start: 0.9374 (mm) cc_final: 0.9149 (mm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1158 time to fit residues: 7.5750 Evaluate side-chains 43 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 153 optimal weight: 0.0070 chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 0.0670 chunk 117 optimal weight: 0.9990 chunk 171 optimal weight: 0.0060 chunk 259 optimal weight: 0.6980 chunk 238 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 21 optimal weight: 5.9990 chunk 159 optimal weight: 0.0010 chunk 126 optimal weight: 8.9990 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 22290 Z= 0.152 Angle : 0.633 7.170 30020 Z= 0.309 Chirality : 0.041 0.146 3400 Planarity : 0.003 0.031 3800 Dihedral : 4.148 17.391 2900 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.17 (0.17), residues: 2520 helix: 1.65 (0.17), residues: 900 sheet: -0.06 (0.29), residues: 420 loop : -1.03 (0.17), residues: 1200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 197 PHE 0.016 0.001 PHE C 121 TYR 0.011 0.001 TYR J 250 ARG 0.003 0.000 ARG B 215 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4536 Ramachandran restraints generated. 2268 Oldfield, 0 Emsley, 2268 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 13 LYS cc_start: 0.8653 (mmmm) cc_final: 0.8253 (mmmm) REVERT: E 50 ASP cc_start: 0.8633 (p0) cc_final: 0.8091 (t70) REVERT: E 85 PHE cc_start: 0.9051 (t80) cc_final: 0.8667 (t80) REVERT: E 120 ASP cc_start: 0.8664 (m-30) cc_final: 0.8375 (m-30) REVERT: E 198 LEU cc_start: 0.9442 (mt) cc_final: 0.9203 (mt) REVERT: E 226 PHE cc_start: 0.8818 (t80) cc_final: 0.8598 (t80) REVERT: E 250 TYR cc_start: 0.8131 (t80) cc_final: 0.7162 (t80) REVERT: E 254 LEU cc_start: 0.9363 (mm) cc_final: 0.9091 (mm) REVERT: E 258 GLN cc_start: 0.8865 (pm20) cc_final: 0.8658 (pm20) outliers start: 0 outliers final: 0 residues processed: 56 average time/residue: 0.1073 time to fit residues: 7.4223 Evaluate side-chains 47 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 260 random chunks: chunk 163 optimal weight: 20.0000 chunk 219 optimal weight: 4.9990 chunk 63 optimal weight: 0.0470 chunk 190 optimal weight: 0.3980 chunk 30 optimal weight: 8.9990 chunk 57 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 86 optimal weight: 1.9990 chunk 212 optimal weight: 8.9990 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 overall best weight: 3.0884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.073388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.057950 restraints weight = 11363.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059927 restraints weight = 7405.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.061367 restraints weight = 5408.141| |-----------------------------------------------------------------------------| r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22290 Z= 0.184 Angle : 0.626 5.884 30020 Z= 0.322 Chirality : 0.042 0.163 3400 Planarity : 0.003 0.029 3800 Dihedral : 4.267 17.393 2900 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % 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: 0.16 (0.17), residues: 2520 helix: 1.52 (0.17), residues: 900 sheet: 0.59 (0.30), residues: 370 loop : -1.14 (0.17), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 197 PHE 0.008 0.001 PHE A 279 TYR 0.012 0.001 TYR G 214 ARG 0.003 0.000 ARG H 215 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2538.22 seconds wall clock time: 48 minutes 8.25 seconds (2888.25 seconds total)