Starting phenix.real_space_refine (version: dev) on Fri Feb 24 02:33:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/02_2023/7kvc_23046.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/02_2023/7kvc_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_23046/02_2023/7kvc_23046.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/02_2023/7kvc_23046.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/02_2023/7kvc_23046.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7kvc_23046/02_2023/7kvc_23046.pdb" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/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: 12.41, per 1000 atoms: 0.57 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: 9.38 Conformation dependent library (CDL) restraints added in 3.3 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: 1.01 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: 6.76 Time building geometry restraints manager: 9.94 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. 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. 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: 0.600 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: 0.020 Extract box with map and model: 4.980 Check model and map are aligned: 0.330 Process input model: 56.770 Find NCS groups from input model: 1.590 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Set scattering table: 0.210 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 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 % 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 *********************** 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 : 0.252 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.0821 time to fit residues: 4.3813 Evaluate side-chains 35 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.290 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3866 ------------------------------------------------------------------------------- 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: 7.9990 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: 4.4388 ------------------------------------------------------------------------------- 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: 0.7962 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 22290 Z= 0.224 Angle : 0.683 5.036 30020 Z= 0.363 Chirality : 0.042 0.126 3400 Planarity : 0.005 0.055 3800 Dihedral : 5.787 22.086 2900 Min Nonbonded Distance : 1.707 Molprobity Statistics. All-atom Clashscore : 27.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer Outliers : 0.40 % 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: -1.85 (0.16), residues: 2520 helix: 0.26 (0.17), residues: 880 sheet: -1.02 (0.26), residues: 370 loop : -2.45 (0.15), residues: 1270 *********************** 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 : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 44 average time/residue: 0.0960 time to fit residues: 5.4359 Evaluate side-chains 41 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0516 time to fit residues: 0.4292 ------------------------------------------------------------------------------- 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: 1.9990 chunk 73 optimal weight: 20.0000 chunk 196 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 65 optimal weight: 0.0670 chunk 236 optimal weight: 6.9990 chunk 255 optimal weight: 0.5980 chunk 210 optimal weight: 8.9990 chunk 234 optimal weight: 20.0000 chunk 80 optimal weight: 7.9990 chunk 189 optimal weight: 30.0000 overall best weight: 3.5324 ------------------------------------------------------------------------------- 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: 0.7955 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 22290 Z= 0.183 Angle : 0.638 5.430 30020 Z= 0.332 Chirality : 0.042 0.119 3400 Planarity : 0.004 0.048 3800 Dihedral : 5.080 21.002 2900 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 22.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.94 % Favored : 92.06 % Rotamer Outliers : 0.40 % 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: -1.39 (0.16), residues: 2520 helix: 0.70 (0.17), residues: 890 sheet: -1.01 (0.26), residues: 350 loop : -2.16 (0.16), residues: 1280 *********************** 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 48 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 47 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 48 average time/residue: 0.1154 time to fit residues: 6.9053 Evaluate side-chains 41 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4006 ------------------------------------------------------------------------------- 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: 5.9990 chunk 177 optimal weight: 20.0000 chunk 122 optimal weight: 0.6980 chunk 26 optimal weight: 20.0000 chunk 112 optimal weight: 0.0060 chunk 158 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 251 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 224 optimal weight: 7.9990 chunk 67 optimal weight: 0.0670 overall best weight: 1.5536 ------------------------------------------------------------------------------- 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: 0.7866 moved from start: 0.2575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 22290 Z= 0.161 Angle : 0.624 5.868 30020 Z= 0.317 Chirality : 0.041 0.110 3400 Planarity : 0.004 0.045 3800 Dihedral : 4.649 18.879 2900 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 17.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.00 % 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: -1.05 (0.17), residues: 2520 helix: 1.20 (0.18), residues: 890 sheet: -0.76 (0.26), residues: 360 loop : -2.18 (0.16), residues: 1270 *********************** 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 51 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.265 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0884 time to fit residues: 5.8639 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 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3933 ------------------------------------------------------------------------------- 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: 10.0000 chunk 142 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 187 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 214 optimal weight: 6.9990 chunk 173 optimal weight: 0.7980 chunk 0 optimal weight: 20.0000 chunk 128 optimal weight: 0.0770 chunk 225 optimal weight: 0.0980 chunk 63 optimal weight: 0.5980 overall best weight: 1.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 57 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: 0.7840 moved from start: 0.2864 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= 0.159 Angle : 0.629 6.081 30020 Z= 0.326 Chirality : 0.043 0.118 3400 Planarity : 0.004 0.043 3800 Dihedral : 4.428 19.090 2900 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.00 % 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: -0.82 (0.17), residues: 2520 helix: 1.26 (0.18), residues: 890 sheet: -0.95 (0.26), residues: 400 loop : -1.82 (0.16), residues: 1230 *********************** 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 51 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1207 time to fit residues: 7.4923 Evaluate side-chains 43 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3656 ------------------------------------------------------------------------------- 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: 5.9990 chunk 226 optimal weight: 3.9990 chunk 49 optimal weight: 0.0020 chunk 147 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 chunk 251 optimal weight: 0.8980 chunk 208 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 overall best weight: 2.1392 ------------------------------------------------------------------------------- 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: 0.7858 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 22290 Z= 0.153 Angle : 0.605 6.060 30020 Z= 0.309 Chirality : 0.041 0.111 3400 Planarity : 0.004 0.040 3800 Dihedral : 4.306 16.293 2900 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer Outliers : 0.00 % 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: -0.63 (0.17), residues: 2520 helix: 1.52 (0.18), residues: 890 sheet: -0.75 (0.27), residues: 400 loop : -1.85 (0.16), residues: 1230 *********************** 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 51 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.285 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.0929 time to fit residues: 6.1231 Evaluate side-chains 43 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 43 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3771 ------------------------------------------------------------------------------- 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: 1.9990 chunk 28 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 183 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 211 optimal weight: 0.0070 chunk 140 optimal weight: 10.0000 chunk 250 optimal weight: 7.9990 chunk 156 optimal weight: 20.0000 chunk 152 optimal weight: 0.2980 chunk 115 optimal weight: 0.6980 overall best weight: 0.5200 ------------------------------------------------------------------------------- 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: 0.7759 moved from start: 0.3656 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= 0.155 Angle : 0.647 6.723 30020 Z= 0.322 Chirality : 0.042 0.141 3400 Planarity : 0.003 0.038 3800 Dihedral : 4.139 18.209 2900 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer Outliers : 0.00 % 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: -0.36 (0.17), residues: 2520 helix: 1.61 (0.18), residues: 890 sheet: -0.80 (0.28), residues: 420 loop : -1.47 (0.17), residues: 1210 *********************** 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 52 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.0909 time to fit residues: 6.1021 Evaluate side-chains 45 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 45 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3629 ------------------------------------------------------------------------------- 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: 7.9990 chunk 100 optimal weight: 8.9990 chunk 149 optimal weight: 0.0030 chunk 75 optimal weight: 0.9980 chunk 49 optimal weight: 0.0070 chunk 48 optimal weight: 0.2980 chunk 159 optimal weight: 0.0270 chunk 170 optimal weight: 9.9990 chunk 123 optimal weight: 9.9990 chunk 23 optimal weight: 7.9990 chunk 196 optimal weight: 9.9990 overall best weight: 0.2666 ------------------------------------------------------------------------------- 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: 0.7696 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 0.035 22290 Z= 0.154 Angle : 0.639 6.843 30020 Z= 0.312 Chirality : 0.041 0.141 3400 Planarity : 0.003 0.028 3800 Dihedral : 4.079 16.753 2900 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.00 % 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: -0.07 (0.17), residues: 2520 helix: 1.73 (0.18), residues: 880 sheet: -0.59 (0.27), residues: 420 loop : -1.19 (0.17), residues: 1220 *********************** 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 53 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1273 time to fit residues: 8.1929 Evaluate side-chains 41 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.257 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3478 ------------------------------------------------------------------------------- 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: 0.0170 chunk 240 optimal weight: 9.9990 chunk 219 optimal weight: 0.3980 chunk 233 optimal weight: 5.9990 chunk 140 optimal weight: 3.9990 chunk 101 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 232 optimal weight: 0.0060 overall best weight: 1.4838 ------------------------------------------------------------------------------- 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: 0.7692 moved from start: 0.4363 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 : 0.672 8.302 30020 Z= 0.339 Chirality : 0.041 0.122 3400 Planarity : 0.003 0.030 3800 Dihedral : 4.304 16.841 2900 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.00 % 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: 0.15 (0.17), residues: 2520 helix: 1.75 (0.18), residues: 890 sheet: -0.30 (0.27), residues: 420 loop : -1.02 (0.17), residues: 1210 *********************** 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 50 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.276 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1234 time to fit residues: 7.5597 Evaluate side-chains 40 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 0.249 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3362 ------------------------------------------------------------------------------- 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: 5.9990 chunk 246 optimal weight: 7.9990 chunk 150 optimal weight: 8.9990 chunk 117 optimal weight: 1.9990 chunk 171 optimal weight: 1.9990 chunk 259 optimal weight: 9.9990 chunk 238 optimal weight: 8.9990 chunk 206 optimal weight: 9.9990 chunk 21 optimal weight: 0.3980 chunk 159 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 overall best weight: 3.6788 ------------------------------------------------------------------------------- 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: 0.7831 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 22290 Z= 0.196 Angle : 0.672 7.858 30020 Z= 0.345 Chirality : 0.042 0.139 3400 Planarity : 0.006 0.079 3800 Dihedral : 4.443 17.113 2900 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 18.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 0.00 % 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: 0.15 (0.17), residues: 2520 helix: 1.75 (0.18), residues: 890 sheet: -0.20 (0.28), residues: 420 loop : -1.06 (0.17), residues: 1210 ********************** 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 46 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1249 time to fit residues: 7.0148 Evaluate side-chains 37 residues out of total 249 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 37 time to evaluate : 0.277 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3539 ------------------------------------------------------------------------------- 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: 0.7980 chunk 63 optimal weight: 0.9980 chunk 190 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 206 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 212 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 38 optimal weight: 7.9990 overall best weight: 5.5586 ------------------------------------------------------------------------------- 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 ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.069532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.054873 restraints weight = 11930.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.056757 restraints weight = 7639.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058066 restraints weight = 5520.279| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 22290 Z= 0.241 Angle : 0.698 6.010 30020 Z= 0.370 Chirality : 0.044 0.165 3400 Planarity : 0.005 0.047 3800 Dihedral : 4.808 17.585 2900 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 24.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 0.00 % 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: -0.15 (0.17), residues: 2520 helix: 1.42 (0.18), residues: 890 sheet: 0.22 (0.29), residues: 400 loop : -1.40 (0.17), residues: 1230 =============================================================================== Job complete usr+sys time: 2296.62 seconds wall clock time: 44 minutes 11.02 seconds (2651.02 seconds total)