Starting phenix.real_space_refine (version: dev) on Sat Feb 25 22:05:35 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2023/6si8_10208_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2023/6si8_10208.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2023/6si8_10208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2023/6si8_10208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2023/6si8_10208_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2023/6si8_10208_trim_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.091 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 ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 174": "OE1" <-> "OE2" Residue "A GLU 191": "OE1" <-> "OE2" Residue "A GLU 225": "OE1" <-> "OE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 134": "OE1" <-> "OE2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B GLU 174": "OE1" <-> "OE2" Residue "B GLU 191": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 234": "OE1" <-> "OE2" Residue "B ARG 322": "NH1" <-> "NH2" Residue "B GLU 370": "OE1" <-> "OE2" Residue "B ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B GLU 392": "OE1" <-> "OE2" Residue "B GLU 401": "OE1" <-> "OE2" Residue "B ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D PHE 90": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D GLU 134": "OE1" <-> "OE2" Residue "D GLU 158": "OE1" <-> "OE2" Residue "D GLU 174": "OE1" <-> "OE2" Residue "D GLU 191": "OE1" <-> "OE2" Residue "D GLU 225": "OE1" <-> "OE2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D GLU 370": "OE1" <-> "OE2" Residue "D ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D GLU 392": "OE1" <-> "OE2" Residue "D GLU 401": "OE1" <-> "OE2" Residue "D ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 134": "OE1" <-> "OE2" Residue "C GLU 158": "OE1" <-> "OE2" Residue "C GLU 174": "OE1" <-> "OE2" Residue "C GLU 191": "OE1" <-> "OE2" Residue "C GLU 225": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ARG 322": "NH1" <-> "NH2" Residue "C GLU 370": "OE1" <-> "OE2" Residue "C ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "C GLU 392": "OE1" <-> "OE2" Residue "C GLU 401": "OE1" <-> "OE2" Residue "C GLU 411": "OE1" <-> "OE2" Residue "C ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 26542 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6584 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6552 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 46 Conformer: "B" Number of residues, atoms: 425, 6552 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 44 Planarities with less than four sites: {'ARG:plan': 3, 'ASN:plan1': 1, 'GLU:plan': 4, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 46 bond proxies already assigned to first conformer: 6590 Chain: "B" Number of atoms: 6599 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6567 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 Conformer: "B" Number of residues, atoms: 425, 6567 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Planarities with less than four sites: {'GLU:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 1, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 45 bond proxies already assigned to first conformer: 6603 Chain: "D" Number of atoms: 6633 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6601 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 Conformer: "B" Number of residues, atoms: 425, 6601 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 32 bond proxies already assigned to first conformer: 6639 Chain: "C" Number of atoms: 6634 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6602 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 Conformer: "B" Number of residues, atoms: 425, 6602 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 29 bond proxies already assigned to first conformer: 6640 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "D" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Chain: "C" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p': 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AALA A 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA A 220 " occ=0.43 residue: pdb=" N AALA B 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA B 220 " occ=0.43 residue: pdb=" N AALA D 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA D 220 " occ=0.43 residue: pdb=" N AALA C 220 " occ=0.57 ... (18 atoms not shown) pdb=" HB3BALA C 220 " occ=0.43 Time building chain proxies: 22.41, per 1000 atoms: 0.84 Number of scatterers: 26542 At special positions: 0 Unit cell: (103.653, 103.653, 105.747, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 86 16.00 P 4 15.00 O 2491 8.00 N 2397 7.00 C 8478 6.00 H 13086 1.00 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: 22.66 Conformation dependent library (CDL) restraints added in 4.3 seconds 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3200 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 24 sheets defined 19.8% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.65 Creating SS restraints... Processing helix chain 'A' and resid 12 through 15 No H-bonds generated for 'chain 'A' and resid 12 through 15' Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 53 through 63 removed outlier: 3.559A pdb=" N ALA A 57 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LEU A 58 " --> pdb=" O ASP A 55 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 59 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N ASN A 60 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE A 62 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ASN A 63 " --> pdb=" O ASN A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 87 Processing helix chain 'A' and resid 93 through 95 No H-bonds generated for 'chain 'A' and resid 93 through 95' Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 149 through 158 removed outlier: 4.405A pdb=" N ILE A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASP A 155 " --> pdb=" O ARG A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 220 through 231 removed outlier: 3.906A pdb=" N GLU A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 243 No H-bonds generated for 'chain 'A' and resid 240 through 243' Processing helix chain 'A' and resid 245 through 251 removed outlier: 3.580A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 290 removed outlier: 4.137A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 403 No H-bonds generated for 'chain 'A' and resid 400 through 403' Processing helix chain 'A' and resid 419 through 424 Processing helix chain 'B' and resid 12 through 15 No H-bonds generated for 'chain 'B' and resid 12 through 15' Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.550A pdb=" N ALA B 57 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LEU B 58 " --> pdb=" O ASP B 55 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER B 59 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN B 60 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE B 62 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ASN B 63 " --> pdb=" O ASN B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 87 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 129 through 131 No H-bonds generated for 'chain 'B' and resid 129 through 131' Processing helix chain 'B' and resid 152 through 158 Processing helix chain 'B' and resid 220 through 227 removed outlier: 3.931A pdb=" N GLU B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 251 removed outlier: 3.595A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 removed outlier: 4.140A pdb=" N LEU B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 403 No H-bonds generated for 'chain 'B' and resid 400 through 403' Processing helix chain 'B' and resid 419 through 424 Processing helix chain 'D' and resid 12 through 15 No H-bonds generated for 'chain 'D' and resid 12 through 15' Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 53 through 63 removed outlier: 3.551A pdb=" N ALA D 57 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LEU D 58 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER D 59 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 5.017A pdb=" N ASN D 60 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ILE D 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN D 63 " --> pdb=" O ASN D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 87 Processing helix chain 'D' and resid 93 through 95 No H-bonds generated for 'chain 'D' and resid 93 through 95' Processing helix chain 'D' and resid 129 through 131 No H-bonds generated for 'chain 'D' and resid 129 through 131' Processing helix chain 'D' and resid 149 through 158 removed outlier: 4.469A pdb=" N ILE D 154 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASP D 155 " --> pdb=" O ARG D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 220 through 231 removed outlier: 3.997A pdb=" N GLU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.599A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 3.511A pdb=" N ASP D 289 " --> pdb=" O LYS D 285 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU D 290 " --> pdb=" O ALA D 286 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 403 No H-bonds generated for 'chain 'D' and resid 400 through 403' Processing helix chain 'D' and resid 419 through 425 removed outlier: 3.780A pdb=" N LEU D 425 " --> pdb=" O MET D 421 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 15 No H-bonds generated for 'chain 'C' and resid 12 through 15' Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 53 through 63 removed outlier: 3.598A pdb=" N ALA C 57 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER C 59 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ASN C 60 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE C 62 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ASN C 63 " --> pdb=" O ASN C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 87 Processing helix chain 'C' and resid 93 through 95 No H-bonds generated for 'chain 'C' and resid 93 through 95' Processing helix chain 'C' and resid 129 through 131 No H-bonds generated for 'chain 'C' and resid 129 through 131' Processing helix chain 'C' and resid 152 through 157 Processing helix chain 'C' and resid 220 through 227 removed outlier: 3.998A pdb=" N GLU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 243 No H-bonds generated for 'chain 'C' and resid 240 through 243' Processing helix chain 'C' and resid 245 through 251 Processing helix chain 'C' and resid 280 through 290 removed outlier: 4.046A pdb=" N LEU C 290 " --> pdb=" O ALA C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 400 through 403 No H-bonds generated for 'chain 'C' and resid 400 through 403' Processing helix chain 'C' and resid 419 through 423 Processing sheet with id= A, first strand: chain 'A' and resid 98 through 101 removed outlier: 7.124A pdb=" N SER A 20 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N GLY A 70 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ALA A 22 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N TYR A 135 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N LEU A 23 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 137 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 215 " --> pdb=" O ALA A 166 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 167 through 171 Processing sheet with id= C, first strand: chain 'A' and resid 179 through 182 removed outlier: 3.544A pdb=" N GLU A 191 " --> pdb=" O ALA A 182 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 317 through 319 Processing sheet with id= E, first strand: chain 'A' and resid 344 through 346 Processing sheet with id= F, first strand: chain 'A' and resid 365 through 367 removed outlier: 6.696A pdb=" N CYS A 382 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL A 415 " --> pdb=" O VAL A 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 98 through 101 removed outlier: 7.296A pdb=" N SER B 20 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.792A pdb=" N GLY B 70 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ALA B 22 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N TYR B 135 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N LEU B 23 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL B 137 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 5.060A pdb=" N ILE B 215 " --> pdb=" O ALA B 166 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 167 through 171 Processing sheet with id= I, first strand: chain 'B' and resid 179 through 182 Processing sheet with id= J, first strand: chain 'B' and resid 317 through 319 Processing sheet with id= K, first strand: chain 'B' and resid 344 through 346 Processing sheet with id= L, first strand: chain 'B' and resid 365 through 367 removed outlier: 6.746A pdb=" N CYS B 382 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 415 " --> pdb=" O VAL B 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 98 through 101 removed outlier: 7.234A pdb=" N SER D 20 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N GLY D 70 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N ALA D 22 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N TYR D 135 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N LEU D 23 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 137 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N ILE D 215 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 167 through 171 Processing sheet with id= O, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.523A pdb=" N GLU D 191 " --> pdb=" O ALA D 182 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 317 through 319 Processing sheet with id= Q, first strand: chain 'D' and resid 344 through 346 Processing sheet with id= R, first strand: chain 'D' and resid 365 through 367 removed outlier: 6.734A pdb=" N CYS D 382 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N VAL D 415 " --> pdb=" O VAL D 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'C' and resid 98 through 101 removed outlier: 7.220A pdb=" N SER C 20 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.748A pdb=" N GLY C 70 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N ALA C 22 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N TYR C 135 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N LEU C 23 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 137 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N ILE C 215 " --> pdb=" O ALA C 166 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 167 through 171 Processing sheet with id= U, first strand: chain 'C' and resid 179 through 182 removed outlier: 3.577A pdb=" N GLU C 191 " --> pdb=" O ALA C 182 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 317 through 319 Processing sheet with id= W, first strand: chain 'C' and resid 344 through 346 Processing sheet with id= X, first strand: chain 'C' and resid 365 through 367 removed outlier: 6.701A pdb=" N CYS C 382 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N VAL C 415 " --> pdb=" O VAL C 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= X 216 hydrogen bonds defined for protein. 621 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: 9.78 Time building geometry restraints manager: 22.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 13050 1.04 - 1.23: 1017 1.23 - 1.43: 4858 1.43 - 1.63: 7783 1.63 - 1.82: 136 Bond restraints: 26844 Sorted by residual: bond pdb=" N VAL C 277 " pdb=" CA VAL C 277 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.32e+00 bond pdb=" N MET D 11 " pdb=" CA MET D 11 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 8.06e+00 bond pdb=" N VAL D 277 " pdb=" CA VAL D 277 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.53e+00 bond pdb=" N VAL B 277 " pdb=" CA VAL B 277 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.25e-02 6.40e+03 7.44e+00 bond pdb=" N HIS D 9 " pdb=" CA HIS D 9 " ideal model delta sigma weight residual 1.454 1.489 -0.034 1.27e-02 6.20e+03 7.36e+00 ... (remaining 26839 not shown) Histogram of bond angle deviations from ideal: 96.81 - 104.71: 380 104.71 - 112.61: 29741 112.61 - 120.50: 9893 120.50 - 128.40: 8187 128.40 - 136.30: 212 Bond angle restraints: 48413 Sorted by residual: angle pdb=" C LEU B 33 " pdb=" N LYS B 34 " pdb=" CA LYS B 34 " ideal model delta sigma weight residual 121.54 130.34 -8.80 1.91e+00 2.74e-01 2.12e+01 angle pdb=" C LEU A 33 " pdb=" N LYS A 34 " pdb=" CA LYS A 34 " ideal model delta sigma weight residual 121.54 130.06 -8.52 1.91e+00 2.74e-01 1.99e+01 angle pdb=" C LEU D 33 " pdb=" N LYS D 34 " pdb=" CA LYS D 34 " ideal model delta sigma weight residual 121.54 129.99 -8.45 1.91e+00 2.74e-01 1.96e+01 angle pdb=" C HIS C 9 " pdb=" N LEU C 10 " pdb=" CA LEU C 10 " ideal model delta sigma weight residual 120.54 126.45 -5.91 1.35e+00 5.49e-01 1.92e+01 angle pdb=" C LEU C 33 " pdb=" N LYS C 34 " pdb=" CA LYS C 34 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.75e+01 ... (remaining 48408 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.87: 10199 24.87 - 49.75: 545 49.75 - 74.62: 67 74.62 - 99.50: 4 99.50 - 124.37: 4 Dihedral angle restraints: 10819 sinusoidal: 5049 harmonic: 5770 Sorted by residual: dihedral pdb=" C5' AMP B 501 " pdb=" O5' AMP B 501 " pdb=" P AMP B 501 " pdb=" O3P AMP B 501 " ideal model delta sinusoidal sigma weight residual -60.00 64.37 -124.37 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" C5' AMP D 501 " pdb=" O5' AMP D 501 " pdb=" P AMP D 501 " pdb=" O3P AMP D 501 " ideal model delta sinusoidal sigma weight residual -60.00 64.30 -124.30 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" C5' AMP C 501 " pdb=" O5' AMP C 501 " pdb=" P AMP C 501 " pdb=" O3P AMP C 501 " ideal model delta sinusoidal sigma weight residual -60.00 -173.36 113.36 1 2.00e+01 2.50e-03 3.35e+01 ... (remaining 10816 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1540 0.081 - 0.161: 454 0.161 - 0.242: 55 0.242 - 0.323: 1 0.323 - 0.403: 2 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CG LEU D 36 " pdb=" CB LEU D 36 " pdb=" CD1 LEU D 36 " pdb=" CD2 LEU D 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.19 -0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CG LEU B 36 " pdb=" CB LEU B 36 " pdb=" CD1 LEU B 36 " pdb=" CD2 LEU B 36 " both_signs ideal model delta sigma weight residual False -2.59 -2.22 -0.37 2.00e-01 2.50e+01 3.49e+00 chirality pdb=" CG LEU A 12 " pdb=" CB LEU A 12 " pdb=" CD1 LEU A 12 " pdb=" CD2 LEU A 12 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.50e+00 ... (remaining 2049 not shown) Planarity restraints: 4060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 407 " 0.007 2.00e-02 2.50e+03 3.87e-02 4.50e+01 pdb=" CG PHE B 407 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 PHE B 407 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE B 407 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE B 407 " 0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE B 407 " -0.041 2.00e-02 2.50e+03 pdb=" CZ PHE B 407 " -0.018 2.00e-02 2.50e+03 pdb=" HD1 PHE B 407 " 0.041 2.00e-02 2.50e+03 pdb=" HD2 PHE B 407 " -0.038 2.00e-02 2.50e+03 pdb=" HE1 PHE B 407 " -0.079 2.00e-02 2.50e+03 pdb=" HE2 PHE B 407 " 0.057 2.00e-02 2.50e+03 pdb=" HZ PHE B 407 " 0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 407 " -0.001 2.00e-02 2.50e+03 3.85e-02 4.44e+01 pdb=" CG PHE A 407 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 PHE A 407 " -0.068 2.00e-02 2.50e+03 pdb=" CD2 PHE A 407 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 PHE A 407 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 PHE A 407 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 407 " 0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE A 407 " 0.054 2.00e-02 2.50e+03 pdb=" HD2 PHE A 407 " -0.047 2.00e-02 2.50e+03 pdb=" HE1 PHE A 407 " 0.027 2.00e-02 2.50e+03 pdb=" HE2 PHE A 407 " 0.062 2.00e-02 2.50e+03 pdb=" HZ PHE A 407 " -0.049 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 273 " -0.032 2.00e-02 2.50e+03 3.84e-02 4.43e+01 pdb=" CG TYR D 273 " -0.018 2.00e-02 2.50e+03 pdb=" CD1 TYR D 273 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 TYR D 273 " -0.032 2.00e-02 2.50e+03 pdb=" CE1 TYR D 273 " 0.022 2.00e-02 2.50e+03 pdb=" CE2 TYR D 273 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR D 273 " -0.016 2.00e-02 2.50e+03 pdb=" OH TYR D 273 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TYR D 273 " 0.080 2.00e-02 2.50e+03 pdb=" HD2 TYR D 273 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 TYR D 273 " -0.043 2.00e-02 2.50e+03 pdb=" HE2 TYR D 273 " 0.065 2.00e-02 2.50e+03 ... (remaining 4057 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.06: 362 2.06 - 2.69: 42453 2.69 - 3.33: 74826 3.33 - 3.96: 101176 3.96 - 4.60: 160129 Nonbonded interactions: 378946 Sorted by model distance: nonbonded pdb=" HD2 TYR D 145 " pdb=" HE1 TRP D 274 " model vdw 1.425 2.100 nonbonded pdb="HD22 LEU B 33 " pdb="HD23 LEU B 36 " model vdw 1.461 2.440 nonbonded pdb="HG11 VAL A 277 " pdb=" HD1 TYR A 283 " model vdw 1.640 2.270 nonbonded pdb=" OD1 ASP A 184 " pdb=" H LYS A 188 " model vdw 1.651 1.850 nonbonded pdb="HH21 ARG B 386 " pdb=" O1P AMP B 501 " model vdw 1.672 1.850 ... (remaining 378941 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 7 through 111 or (resid 112 through 113 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 114 through \ 150 or resid 152 through 219 or resid 222 through 384 or (resid 385 and (name N \ or name CA or name C or name O or name CB or name H or name HA )) or resid 386 \ through 431 or resid 501)) selection = (chain 'B' and (resid 7 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 30 through 106 or (resid \ 107 through 109 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 110 through 150 or resid 152 through 219 or resid 222 thr \ ough 266 or (resid 267 and (name N or name CA or name C or name O or name CB or \ name H or name HA )) or resid 268 through 384 or (resid 385 and (name N or name \ CA or name C or name O or name CB or name H or name HA )) or resid 386 through 4 \ 31 or resid 501)) selection = (chain 'C' and (resid 7 through 106 or (resid 107 through 109 and (name N or nam \ e CA or name C or name O or name CB or name H or name HA )) or resid 110 through \ 111 or (resid 112 through 113 and (name N or name CA or name C or name O or nam \ e CB or name H or name HA )) or resid 114 or (resid 115 and (name N or name CA o \ r name C or name O or name CB or name H or name HA )) or resid 116 through 150 o \ r resid 152 through 193 or (resid 194 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 195 through 219 or resid 222 throug \ h 266 or (resid 267 and (name N or name CA or name C or name O or name CB or nam \ e H or name HA )) or resid 268 through 384 or (resid 385 and (name N or name CA \ or name C or name O or name CB or name H or name HA )) or resid 386 through 431 \ or resid 501)) selection = (chain 'D' and (resid 7 through 28 or (resid 29 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 30 through 106 or (resid \ 107 through 109 and (name N or name CA or name C or name O or name CB or name H \ or name HA )) or resid 110 through 111 or (resid 112 through 113 and (name N or \ name CA or name C or name O or name CB or name H or name HA )) or resid 114 thro \ ugh 150 or resid 152 through 193 or (resid 194 and (name N or name CA or name C \ or name O or name CB or name H or name HA )) or resid 195 through 219 or resid 2 \ 22 through 266 or (resid 267 and (name N or name CA or name C or name O or name \ CB or name H or name HA )) or resid 268 through 431 or resid 501)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 4 5.49 5 S 86 5.16 5 C 8478 2.51 5 N 2397 2.21 5 O 2491 1.98 5 H 13086 0.53 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=0.43 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.480 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: 0.440 Extract box with map and model: 4.050 Check model and map are aligned: 0.370 Process input model: 93.490 Find NCS groups from input model: 1.490 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Set scattering table: 0.230 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 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 : 0.010 0.094 13758 Z= 0.688 Angle : 1.113 8.802 18678 Z= 0.628 Chirality : 0.072 0.403 2052 Planarity : 0.009 0.060 2436 Dihedral : 14.587 124.373 5126 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.35 % Allowed : 8.33 % Favored : 91.31 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.17), residues: 1708 helix: -3.81 (0.15), residues: 412 sheet: -2.74 (0.25), residues: 336 loop : -1.79 (0.18), residues: 960 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 413 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 382 time to evaluate : 2.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 7 residues processed: 397 average time/residue: 0.7564 time to fit residues: 405.7898 Evaluate side-chains 222 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 2.110 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.6407 time to fit residues: 8.9762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.6980 chunk 85 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 9 HIS B 235 ASN ** B 257 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 GLN C 76 GLN C 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 13758 Z= 0.167 Angle : 0.625 6.039 18678 Z= 0.319 Chirality : 0.046 0.162 2052 Planarity : 0.005 0.059 2436 Dihedral : 7.333 88.143 1938 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.36 % Favored : 97.58 % Rotamer Outliers : 1.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.18), residues: 1708 helix: -2.59 (0.21), residues: 408 sheet: -1.41 (0.36), residues: 188 loop : -1.55 (0.17), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 247 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 235 time to evaluate : 2.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 241 average time/residue: 0.6527 time to fit residues: 221.1200 Evaluate side-chains 208 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 200 time to evaluate : 2.158 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.3314 time to fit residues: 7.5586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 42 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 52 optimal weight: 20.0000 chunk 122 optimal weight: 4.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 347 GLN B 204 ASN B 235 ASN D 63 ASN D 147 GLN C 9 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 13758 Z= 0.446 Angle : 0.665 6.485 18678 Z= 0.342 Chirality : 0.049 0.153 2052 Planarity : 0.005 0.054 2436 Dihedral : 6.991 70.126 1938 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.97 % Favored : 93.91 % Rotamer Outliers : 2.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.19), residues: 1708 helix: -2.12 (0.23), residues: 408 sheet: -1.23 (0.36), residues: 192 loop : -1.60 (0.17), residues: 1108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 227 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 199 time to evaluate : 2.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 17 residues processed: 217 average time/residue: 0.6293 time to fit residues: 193.6638 Evaluate side-chains 202 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 2.162 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.2986 time to fit residues: 11.9547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 2.9990 chunk 114 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 102 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 0.7980 chunk 145 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 235 ASN ** D 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 347 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 13758 Z= 0.188 Angle : 0.569 6.119 18678 Z= 0.284 Chirality : 0.045 0.154 2052 Planarity : 0.004 0.057 2436 Dihedral : 6.547 65.411 1938 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.19), residues: 1708 helix: -1.50 (0.25), residues: 408 sheet: -0.92 (0.36), residues: 188 loop : -1.29 (0.18), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 208 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 201 time to evaluate : 2.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 202 average time/residue: 0.6225 time to fit residues: 183.8769 Evaluate side-chains 184 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 183 time to evaluate : 2.139 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3710 time to fit residues: 3.4062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.4980 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 0.2980 chunk 112 optimal weight: 0.5980 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 0.4980 chunk 40 optimal weight: 4.9990 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN B 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 13758 Z= 0.141 Angle : 0.542 5.940 18678 Z= 0.267 Chirality : 0.045 0.177 2052 Planarity : 0.004 0.046 2436 Dihedral : 6.180 63.934 1938 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.20), residues: 1708 helix: -1.02 (0.27), residues: 408 sheet: -0.73 (0.36), residues: 188 loop : -1.10 (0.18), residues: 1112 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 197 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 191 time to evaluate : 2.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 193 average time/residue: 0.6170 time to fit residues: 170.6535 Evaluate side-chains 184 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 179 time to evaluate : 2.119 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3211 time to fit residues: 5.4986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 3.9990 chunk 146 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN D 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 13758 Z= 0.286 Angle : 0.573 5.871 18678 Z= 0.286 Chirality : 0.046 0.144 2052 Planarity : 0.004 0.038 2436 Dihedral : 6.225 65.428 1938 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.44 % Favored : 94.50 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.55 (0.20), residues: 1708 helix: -0.92 (0.27), residues: 408 sheet: -0.82 (0.34), residues: 196 loop : -1.12 (0.18), residues: 1104 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 179 average time/residue: 0.6227 time to fit residues: 160.4245 Evaluate side-chains 168 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 164 time to evaluate : 2.128 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.3229 time to fit residues: 5.1481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 161 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 13758 Z= 0.237 Angle : 0.551 5.965 18678 Z= 0.273 Chirality : 0.045 0.143 2052 Planarity : 0.004 0.039 2436 Dihedral : 6.130 64.392 1938 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.20), residues: 1708 helix: -0.85 (0.27), residues: 416 sheet: -0.80 (0.34), residues: 196 loop : -1.05 (0.18), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 173 time to evaluate : 2.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 175 average time/residue: 0.6581 time to fit residues: 163.8941 Evaluate side-chains 165 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 2.199 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.7624 time to fit residues: 5.8584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 110 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 13758 Z= 0.231 Angle : 0.548 5.980 18678 Z= 0.271 Chirality : 0.045 0.143 2052 Planarity : 0.004 0.084 2436 Dihedral : 6.082 63.703 1938 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.26 % Favored : 94.68 % Rotamer Outliers : 0.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.20), residues: 1708 helix: -0.74 (0.27), residues: 416 sheet: -0.73 (0.34), residues: 196 loop : -0.98 (0.19), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 168 time to evaluate : 2.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 171 average time/residue: 0.6561 time to fit residues: 159.8246 Evaluate side-chains 165 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 2.375 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 3 average time/residue: 0.7506 time to fit residues: 5.8562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.6980 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 90 optimal weight: 4.9990 chunk 65 optimal weight: 0.4980 chunk 118 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 142 optimal weight: 0.5980 chunk 99 optimal weight: 0.0270 chunk 159 optimal weight: 4.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.4467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 13758 Z= 0.138 Angle : 0.525 5.836 18678 Z= 0.256 Chirality : 0.044 0.140 2052 Planarity : 0.003 0.072 2436 Dihedral : 5.858 61.171 1938 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.01 % Favored : 96.93 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.06 (0.20), residues: 1708 helix: -0.43 (0.28), residues: 416 sheet: -0.59 (0.34), residues: 196 loop : -0.82 (0.19), residues: 1096 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 169 time to evaluate : 2.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 170 average time/residue: 0.6723 time to fit residues: 162.9236 Evaluate side-chains 167 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 165 time to evaluate : 2.230 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.9439 time to fit residues: 5.0440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 110 optimal weight: 0.4980 chunk 167 optimal weight: 2.9990 chunk 154 optimal weight: 0.8980 chunk 133 optimal weight: 0.2980 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN D 287 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.4535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 13758 Z= 0.133 Angle : 0.522 5.788 18678 Z= 0.253 Chirality : 0.044 0.140 2052 Planarity : 0.003 0.030 2436 Dihedral : 5.707 59.380 1938 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.90 % Favored : 97.04 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.20), residues: 1708 helix: -0.25 (0.28), residues: 416 sheet: -0.47 (0.34), residues: 196 loop : -0.71 (0.19), residues: 1096 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3416 Ramachandran restraints generated. 1708 Oldfield, 0 Emsley, 1708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Residue MET 108 is missing expected H atoms. Skipping. Residue LYS 109 is missing expected H atoms. Skipping. Evaluate side-chains 174 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 170 time to evaluate : 2.515 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 173 average time/residue: 0.6425 time to fit residues: 159.3411 Evaluate side-chains 163 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 2.148 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 1.4800 time to fit residues: 4.4485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 5.9990 chunk 122 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 37 optimal weight: 0.9980 chunk 133 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 117 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN B 235 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.161531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.130790 restraints weight = 105339.583| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 4.21 r_work: 0.3434 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3950 r_free = 0.3950 target_work(ls_wunit_k1) = 0.162 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.4610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 13758 Z= 0.139 Angle : 0.523 6.128 18678 Z= 0.253 Chirality : 0.044 0.144 2052 Planarity : 0.004 0.097 2436 Dihedral : 5.627 58.415 1938 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.84 % Favored : 97.10 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.84 (0.20), residues: 1708 helix: -0.16 (0.28), residues: 420 sheet: -0.42 (0.35), residues: 196 loop : -0.73 (0.19), residues: 1092 =============================================================================== Job complete usr+sys time: 5846.11 seconds wall clock time: 104 minutes 49.08 seconds (6289.08 seconds total)