Starting phenix.real_space_refine on Tue Feb 20 02:00:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2024/6si8_10208_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2024/6si8_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_2024/6si8_10208.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2024/6si8_10208.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2024/6si8_10208_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6si8_10208/02_2024/6si8_10208_trim_updated.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 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. 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-5238/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: 22.45, per 1000 atoms: 0.85 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: 21.15 Conformation dependent library (CDL) restraints added in 5.7 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: 4.14 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: 9.74 Time building geometry restraints manager: 21.75 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: 11858 24.87 - 49.75: 710 49.75 - 74.62: 95 74.62 - 99.50: 4 99.50 - 124.37: 4 Dihedral angle restraints: 12671 sinusoidal: 6901 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 12668 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 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: 0.000 Normalize map: mean=0, sd=1: 0.490 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: 0.430 Extract box with map and model: 3.370 Check model and map are aligned: 0.410 Set scattering table: 0.240 Process input model: 97.650 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 106.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 % Allowed : 8.13 % Favored : 89.42 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.010 TRP C 274 HIS 0.033 0.007 HIS A 156 PHE 0.047 0.011 PHE A 98 TYR 0.040 0.009 TYR A 273 ARG 0.058 0.005 ARG C 130 *********************** 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 : 2.031 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 REVERT: A 123 GLN cc_start: 0.8166 (OUTLIER) cc_final: 0.7115 (mp10) REVERT: A 243 ASP cc_start: 0.7190 (m-30) cc_final: 0.6943 (m-30) REVERT: B 162 ARG cc_start: 0.7551 (mmm-85) cc_final: 0.7323 (mmm-85) REVERT: B 328 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6930 (mtm) REVERT: D 14 ARG cc_start: 0.8393 (ttp80) cc_final: 0.8114 (ttp80) REVERT: D 82 GLN cc_start: 0.8197 (tt0) cc_final: 0.7602 (tt0) REVERT: D 92 ASN cc_start: 0.7729 (m-40) cc_final: 0.7180 (p0) REVERT: D 117 THR cc_start: 0.9046 (m) cc_final: 0.8646 (p) REVERT: D 184 ASP cc_start: 0.7777 (p0) cc_final: 0.6938 (p0) REVERT: D 187 ASP cc_start: 0.6681 (m-30) cc_final: 0.6479 (m-30) REVERT: D 341 SER cc_start: 0.8667 (m) cc_final: 0.8347 (t) REVERT: D 359 PHE cc_start: 0.8790 (m-80) cc_final: 0.8536 (m-80) REVERT: C 67 ARG cc_start: 0.8283 (mtp85) cc_final: 0.8063 (mtt90) REVERT: C 105 GLN cc_start: 0.7580 (mm110) cc_final: 0.7279 (mm110) REVERT: C 180 VAL cc_start: 0.9049 (t) cc_final: 0.8640 (m) REVERT: C 212 SER cc_start: 0.8773 (t) cc_final: 0.8094 (p) REVERT: C 309 TYR cc_start: 0.7945 (t80) cc_final: 0.7583 (t80) outliers start: 31 outliers final: 7 residues processed: 397 average time/residue: 0.7387 time to fit residues: 395.3785 Evaluate side-chains 232 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 223 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 328 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.9990 chunk 127 optimal weight: 0.7980 chunk 70 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.4980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 152 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 D 123 GLN C 76 GLN C 82 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13758 Z= 0.168 Angle : 0.627 6.107 18678 Z= 0.322 Chirality : 0.046 0.157 2052 Planarity : 0.005 0.053 2436 Dihedral : 8.351 90.237 1965 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.96 % Favored : 96.99 % Rotamer: Outliers : 1.47 % Allowed : 13.03 % Favored : 85.49 % 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: -2.71 (0.18), residues: 1708 helix: -2.68 (0.21), residues: 416 sheet: -1.45 (0.36), residues: 188 loop : -1.52 (0.17), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 284 HIS 0.008 0.001 HIS A 257 PHE 0.017 0.001 PHE D 178 TYR 0.015 0.001 TYR C 75 ARG 0.005 0.001 ARG B 32 *********************** 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 253 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 236 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 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: A 86 ARG cc_start: 0.8342 (mtt180) cc_final: 0.7822 (mtm180) REVERT: B 19 LYS cc_start: 0.7673 (mttt) cc_final: 0.7393 (mtmt) REVERT: B 34 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8596 (mmmm) REVERT: B 178 PHE cc_start: 0.7609 (m-80) cc_final: 0.7223 (m-80) REVERT: B 406 ARG cc_start: 0.8935 (mtp180) cc_final: 0.8609 (mtm180) REVERT: B 421 MET cc_start: 0.8050 (mtt) cc_final: 0.7780 (mtt) REVERT: D 11 MET cc_start: 0.8305 (mmm) cc_final: 0.8045 (tpp) REVERT: D 14 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8146 (ttp80) REVERT: D 117 THR cc_start: 0.9027 (m) cc_final: 0.8634 (p) REVERT: D 328 MET cc_start: 0.7122 (OUTLIER) cc_final: 0.6888 (mtt) REVERT: D 341 SER cc_start: 0.8634 (m) cc_final: 0.8344 (t) REVERT: D 421 MET cc_start: 0.8226 (mtt) cc_final: 0.7947 (mtt) REVERT: C 180 VAL cc_start: 0.8512 (t) cc_final: 0.8064 (m) REVERT: C 212 SER cc_start: 0.8859 (t) cc_final: 0.8159 (p) REVERT: C 309 TYR cc_start: 0.7930 (t80) cc_final: 0.7701 (t80) outliers start: 17 outliers final: 11 residues processed: 246 average time/residue: 0.6932 time to fit residues: 240.4432 Evaluate side-chains 217 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 205 time to evaluate : 2.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 198 ASN Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 126 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 126 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 chunk 152 optimal weight: 4.9990 chunk 165 optimal weight: 7.9990 chunk 136 optimal weight: 10.0000 chunk 151 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 122 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 GLN A 112 ASN A 347 GLN B 204 ASN B 235 ASN B 347 GLN ** D 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 GLN D 347 GLN C 9 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.3375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 13758 Z= 0.490 Angle : 0.689 6.528 18678 Z= 0.358 Chirality : 0.050 0.153 2052 Planarity : 0.006 0.066 2436 Dihedral : 7.889 68.320 1957 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.50 % Favored : 93.38 % Rotamer: Outliers : 2.66 % Allowed : 12.75 % Favored : 84.58 % 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: -2.63 (0.19), residues: 1708 helix: -2.30 (0.22), residues: 416 sheet: -1.25 (0.36), residues: 192 loop : -1.65 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 284 HIS 0.010 0.001 HIS A 257 PHE 0.018 0.002 PHE A 192 TYR 0.023 0.002 TYR C 75 ARG 0.009 0.001 ARG C 67 *********************** 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 231 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 197 time to evaluate : 2.310 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: A 86 ARG cc_start: 0.8318 (mtt180) cc_final: 0.7908 (ttm170) REVERT: A 94 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8281 (pt0) REVERT: A 421 MET cc_start: 0.8890 (mtt) cc_final: 0.8471 (mtt) REVERT: B 34 LYS cc_start: 0.9017 (mmtt) cc_final: 0.8743 (mmmm) REVERT: B 233 ASP cc_start: 0.8493 (m-30) cc_final: 0.7918 (t0) REVERT: D 14 ARG cc_start: 0.8567 (ttp80) cc_final: 0.8303 (ttp80) REVERT: D 174 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7224 (tm-30) REVERT: D 289 ASP cc_start: 0.8495 (t70) cc_final: 0.8146 (t0) REVERT: D 328 MET cc_start: 0.7416 (mtm) cc_final: 0.7152 (mtt) REVERT: D 341 SER cc_start: 0.8784 (m) cc_final: 0.8480 (t) REVERT: D 359 PHE cc_start: 0.9050 (m-80) cc_final: 0.8807 (m-80) REVERT: C 212 SER cc_start: 0.9104 (t) cc_final: 0.8493 (p) REVERT: C 309 TYR cc_start: 0.8192 (t80) cc_final: 0.7974 (t80) outliers start: 34 outliers final: 20 residues processed: 223 average time/residue: 0.6526 time to fit residues: 203.7847 Evaluate side-chains 203 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 182 time to evaluate : 2.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 164 THR Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 89 SER Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 352 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 1.9990 chunk 114 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 102 optimal weight: 7.9990 chunk 153 optimal weight: 0.9990 chunk 162 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 235 ASN D 63 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3649 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= 0.177 Angle : 0.568 6.104 18678 Z= 0.284 Chirality : 0.045 0.153 2052 Planarity : 0.004 0.067 2436 Dihedral : 7.178 66.932 1948 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.66 % Favored : 97.28 % Rotamer: Outliers : 1.26 % Allowed : 14.23 % Favored : 84.51 % 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: -2.05 (0.19), residues: 1708 helix: -1.71 (0.24), residues: 416 sheet: -0.91 (0.36), residues: 188 loop : -1.32 (0.18), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 284 HIS 0.003 0.001 HIS A 257 PHE 0.015 0.001 PHE D 51 TYR 0.016 0.001 TYR D 131 ARG 0.007 0.000 ARG C 67 *********************** 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 205 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 191 time to evaluate : 2.294 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: A 86 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7902 (ttm170) REVERT: A 421 MET cc_start: 0.8855 (mtt) cc_final: 0.8432 (mtp) REVERT: B 34 LYS cc_start: 0.8984 (mmtt) cc_final: 0.8746 (mmmm) REVERT: B 225 GLU cc_start: 0.8055 (tp30) cc_final: 0.7814 (tp30) REVERT: B 228 GLU cc_start: 0.7095 (tm-30) cc_final: 0.6834 (tm-30) REVERT: B 233 ASP cc_start: 0.8424 (m-30) cc_final: 0.7927 (t0) REVERT: D 174 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7088 (tm-30) REVERT: D 194 GLU cc_start: 0.6345 (tm-30) cc_final: 0.6090 (tm-30) REVERT: D 289 ASP cc_start: 0.8485 (t70) cc_final: 0.8141 (t0) REVERT: D 328 MET cc_start: 0.7380 (mtm) cc_final: 0.7128 (mtt) REVERT: D 341 SER cc_start: 0.8700 (m) cc_final: 0.8385 (t) REVERT: D 359 PHE cc_start: 0.8981 (m-80) cc_final: 0.8717 (m-80) REVERT: C 34 LYS cc_start: 0.9260 (mmtt) cc_final: 0.8983 (mmmm) REVERT: C 212 SER cc_start: 0.9155 (t) cc_final: 0.8471 (p) REVERT: C 309 TYR cc_start: 0.8136 (t80) cc_final: 0.7925 (t80) outliers start: 14 outliers final: 10 residues processed: 200 average time/residue: 0.6454 time to fit residues: 185.9640 Evaluate side-chains 194 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 184 time to evaluate : 2.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 328 MET Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 73 THR Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 323 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 0.0570 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 8.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 overall best weight: 2.7704 ------------------------------------------------------------------------------- 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: 0.7711 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13758 Z= 0.321 Angle : 0.590 5.869 18678 Z= 0.298 Chirality : 0.046 0.149 2052 Planarity : 0.005 0.057 2436 Dihedral : 7.032 67.503 1948 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.80 % Favored : 93.14 % Rotamer: Outliers : 1.96 % Allowed : 13.95 % Favored : 84.09 % 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: -1.95 (0.19), residues: 1708 helix: -1.44 (0.26), residues: 416 sheet: -0.95 (0.35), residues: 196 loop : -1.32 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.003 0.001 HIS D 9 PHE 0.014 0.002 PHE C 178 TYR 0.022 0.001 TYR D 114 ARG 0.007 0.001 ARG C 67 *********************** 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 202 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 178 time to evaluate : 2.040 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: A 86 ARG cc_start: 0.8256 (mtt180) cc_final: 0.8038 (ttm170) REVERT: A 299 MET cc_start: 0.8248 (mmm) cc_final: 0.7906 (mmm) REVERT: B 34 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8806 (mmmm) REVERT: B 233 ASP cc_start: 0.8446 (m-30) cc_final: 0.7961 (t0) REVERT: D 194 GLU cc_start: 0.6397 (tm-30) cc_final: 0.6112 (tm-30) REVERT: D 289 ASP cc_start: 0.8551 (t70) cc_final: 0.8351 (t0) REVERT: D 328 MET cc_start: 0.7488 (mtm) cc_final: 0.7254 (mtt) REVERT: D 341 SER cc_start: 0.8718 (m) cc_final: 0.8397 (t) REVERT: D 359 PHE cc_start: 0.8985 (m-80) cc_final: 0.8713 (m-80) REVERT: C 34 LYS cc_start: 0.9279 (mmtt) cc_final: 0.8975 (mmmm) REVERT: C 212 SER cc_start: 0.9110 (t) cc_final: 0.8521 (p) REVERT: C 309 TYR cc_start: 0.8187 (t80) cc_final: 0.7983 (t80) outliers start: 24 outliers final: 17 residues processed: 194 average time/residue: 0.6284 time to fit residues: 173.6211 Evaluate side-chains 184 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 167 time to evaluate : 2.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 310 ASN Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 323 SER 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: 3.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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: 0.7714 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13758 Z= 0.289 Angle : 0.572 5.979 18678 Z= 0.287 Chirality : 0.046 0.195 2052 Planarity : 0.004 0.056 2436 Dihedral : 6.906 67.004 1948 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.61 % Favored : 95.33 % Rotamer: Outliers : 1.61 % Allowed : 14.65 % Favored : 83.74 % 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: -1.73 (0.20), residues: 1708 helix: -1.22 (0.26), residues: 416 sheet: -0.94 (0.34), residues: 196 loop : -1.16 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 284 HIS 0.005 0.001 HIS A 427 PHE 0.013 0.001 PHE A 192 TYR 0.017 0.001 TYR C 75 ARG 0.005 0.000 ARG C 67 *********************** 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 191 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 172 time to evaluate : 2.101 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: A 86 ARG cc_start: 0.8265 (mtt180) cc_final: 0.8063 (ttm170) REVERT: A 299 MET cc_start: 0.8274 (mmm) cc_final: 0.7947 (mmm) REVERT: B 34 LYS cc_start: 0.8995 (mmtt) cc_final: 0.8755 (mmmm) REVERT: B 233 ASP cc_start: 0.8472 (m-30) cc_final: 0.8029 (t0) REVERT: B 355 ARG cc_start: 0.7563 (ttm-80) cc_final: 0.7359 (ttm-80) REVERT: D 194 GLU cc_start: 0.6383 (tm-30) cc_final: 0.6075 (tm-30) REVERT: D 289 ASP cc_start: 0.8573 (t70) cc_final: 0.8241 (t0) REVERT: D 328 MET cc_start: 0.7521 (mtm) cc_final: 0.7216 (mtt) REVERT: D 341 SER cc_start: 0.8696 (m) cc_final: 0.8387 (t) REVERT: C 34 LYS cc_start: 0.9287 (mmtt) cc_final: 0.8956 (mmmm) REVERT: C 212 SER cc_start: 0.9110 (t) cc_final: 0.8494 (p) REVERT: C 403 ASP cc_start: 0.8003 (m-30) cc_final: 0.7743 (m-30) outliers start: 19 outliers final: 17 residues processed: 188 average time/residue: 0.7164 time to fit residues: 190.8220 Evaluate side-chains 183 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 166 time to evaluate : 2.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 264 VAL Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 152 MET Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain C residue 20 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 92 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 chunk 161 optimal weight: 4.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13758 Z= 0.298 Angle : 0.568 6.065 18678 Z= 0.285 Chirality : 0.046 0.147 2052 Planarity : 0.004 0.071 2436 Dihedral : 6.849 65.793 1948 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.06 % Allowed : 6.91 % Favored : 93.03 % Rotamer: Outliers : 1.96 % Allowed : 14.44 % Favored : 83.60 % 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: -1.66 (0.20), residues: 1708 helix: -1.06 (0.26), residues: 416 sheet: -0.85 (0.34), residues: 196 loop : -1.18 (0.18), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 284 HIS 0.004 0.001 HIS A 257 PHE 0.012 0.001 PHE A 192 TYR 0.016 0.001 TYR C 75 ARG 0.011 0.000 ARG C 67 *********************** 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 194 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 2.190 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: A 299 MET cc_start: 0.8302 (mmm) cc_final: 0.7992 (mmm) REVERT: B 34 LYS cc_start: 0.9013 (mmtt) cc_final: 0.8761 (mmmm) REVERT: B 355 ARG cc_start: 0.7573 (ttm-80) cc_final: 0.7353 (ttm-80) REVERT: D 174 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7180 (tm-30) REVERT: D 194 GLU cc_start: 0.6406 (tm-30) cc_final: 0.6089 (tm-30) REVERT: D 328 MET cc_start: 0.7548 (mtm) cc_final: 0.7241 (mtt) REVERT: D 341 SER cc_start: 0.8702 (m) cc_final: 0.8395 (t) outliers start: 25 outliers final: 20 residues processed: 190 average time/residue: 0.6898 time to fit residues: 182.9383 Evaluate side-chains 185 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 165 time to evaluate : 3.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 279 THR Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain B residue 97 GLU Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 377 CYS Chi-restraints excluded: chain B residue 386 ARG Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 20 SER Chi-restraints excluded: chain D residue 84 ILE Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 229 GLU Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 164 THR Chi-restraints excluded: chain C residue 352 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 110 optimal weight: 0.0010 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 127 optimal weight: 0.6980 chunk 147 optimal weight: 0.8980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 13758 Z= 0.134 Angle : 0.529 5.875 18678 Z= 0.260 Chirality : 0.044 0.141 2052 Planarity : 0.004 0.066 2436 Dihedral : 6.525 62.363 1948 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.72 % Favored : 97.22 % Rotamer: Outliers : 1.05 % Allowed : 15.21 % Favored : 83.74 % 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: -1.22 (0.20), residues: 1708 helix: -0.59 (0.28), residues: 416 sheet: -0.70 (0.34), residues: 196 loop : -0.90 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.004 0.001 HIS A 257 PHE 0.011 0.001 PHE D 178 TYR 0.014 0.001 TYR C 75 ARG 0.008 0.000 ARG C 67 *********************** 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 183 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 171 time to evaluate : 2.533 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: B 34 LYS cc_start: 0.8948 (mmtt) cc_final: 0.8712 (mmmm) REVERT: B 355 ARG cc_start: 0.7511 (ttm-80) cc_final: 0.7291 (ttm-80) REVERT: D 194 GLU cc_start: 0.6365 (tm-30) cc_final: 0.6009 (tm-30) REVERT: D 289 ASP cc_start: 0.8537 (t70) cc_final: 0.8224 (t0) REVERT: D 328 MET cc_start: 0.7486 (mtm) cc_final: 0.7195 (mtt) REVERT: C 309 TYR cc_start: 0.8201 (t80) cc_final: 0.7926 (t80) outliers start: 12 outliers final: 10 residues processed: 182 average time/residue: 0.6638 time to fit residues: 170.2836 Evaluate side-chains 174 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 164 time to evaluate : 2.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 360 CYS Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG Chi-restraints excluded: chain C residue 352 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 90 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 136 optimal weight: 0.0970 chunk 142 optimal weight: 0.9980 chunk 99 optimal weight: 0.7980 chunk 159 optimal weight: 3.9990 overall best weight: 0.5956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.4485 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= 0.135 Angle : 0.522 5.860 18678 Z= 0.254 Chirality : 0.044 0.143 2052 Planarity : 0.004 0.060 2436 Dihedral : 6.358 60.300 1948 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.19 % Favored : 96.75 % Rotamer: Outliers : 0.77 % Allowed : 15.35 % Favored : 83.88 % 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: -0.99 (0.20), residues: 1708 helix: -0.36 (0.28), residues: 416 sheet: -0.51 (0.34), residues: 196 loop : -0.79 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 274 HIS 0.003 0.000 HIS A 257 PHE 0.011 0.001 PHE D 51 TYR 0.016 0.001 TYR C 75 ARG 0.008 0.000 ARG C 67 *********************** 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 179 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 171 time to evaluate : 2.070 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: B 34 LYS cc_start: 0.8960 (mmtt) cc_final: 0.8725 (mmmm) REVERT: B 97 GLU cc_start: 0.8124 (pt0) cc_final: 0.7890 (pm20) REVERT: B 233 ASP cc_start: 0.8395 (m-30) cc_final: 0.7861 (t0) REVERT: B 355 ARG cc_start: 0.7506 (ttm-80) cc_final: 0.7187 (tpp-160) REVERT: D 174 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7077 (tm-30) REVERT: D 194 GLU cc_start: 0.6371 (tm-30) cc_final: 0.6004 (tm-30) REVERT: D 289 ASP cc_start: 0.8523 (t70) cc_final: 0.8233 (t0) REVERT: D 328 MET cc_start: 0.7515 (mtm) cc_final: 0.7253 (mtt) REVERT: C 428 LYS cc_start: 0.8396 (ttpt) cc_final: 0.8136 (tttm) outliers start: 8 outliers final: 6 residues processed: 178 average time/residue: 0.6517 time to fit residues: 161.8267 Evaluate side-chains 172 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 166 time to evaluate : 1.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG 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: 1.9990 chunk 110 optimal weight: 3.9990 chunk 167 optimal weight: 0.0470 chunk 154 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 102 optimal weight: 0.0050 chunk 81 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 overall best weight: 0.7094 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13758 Z= 0.135 Angle : 0.517 5.789 18678 Z= 0.251 Chirality : 0.044 0.143 2052 Planarity : 0.004 0.061 2436 Dihedral : 6.214 58.736 1948 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 2.78 % Favored : 97.16 % Rotamer: Outliers : 0.63 % Allowed : 15.84 % Favored : 83.53 % 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: -0.81 (0.20), residues: 1708 helix: -0.16 (0.28), residues: 416 sheet: -0.36 (0.34), residues: 196 loop : -0.70 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 274 HIS 0.003 0.000 HIS A 427 PHE 0.007 0.001 PHE D 178 TYR 0.017 0.001 TYR C 75 ARG 0.007 0.000 ARG C 67 ********************** 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 178 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 172 time to evaluate : 2.173 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: B 34 LYS cc_start: 0.8930 (mmtt) cc_final: 0.8693 (mmmm) REVERT: B 97 GLU cc_start: 0.8135 (pt0) cc_final: 0.7915 (pm20) REVERT: B 225 GLU cc_start: 0.7903 (tp30) cc_final: 0.7637 (tp30) REVERT: B 233 ASP cc_start: 0.8359 (m-30) cc_final: 0.7861 (t0) REVERT: B 355 ARG cc_start: 0.7510 (ttm-80) cc_final: 0.7188 (tpp-160) REVERT: D 174 GLU cc_start: 0.7781 (tm-30) cc_final: 0.7119 (tm-30) REVERT: D 194 GLU cc_start: 0.6351 (tm-30) cc_final: 0.5979 (tm-30) REVERT: D 289 ASP cc_start: 0.8520 (t70) cc_final: 0.8189 (t0) REVERT: D 328 MET cc_start: 0.7536 (mtm) cc_final: 0.7283 (mtt) REVERT: C 309 TYR cc_start: 0.8209 (t80) cc_final: 0.7917 (t80) REVERT: C 428 LYS cc_start: 0.8363 (ttpt) cc_final: 0.8113 (tttm) outliers start: 6 outliers final: 5 residues processed: 178 average time/residue: 0.6624 time to fit residues: 165.2828 Evaluate side-chains 173 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 168 time to evaluate : 1.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 405 ARG Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 244 LEU Chi-restraints excluded: chain D residue 386 ARG 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: 0.8980 chunk 19 optimal weight: 0.0570 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 0.5980 chunk 55 optimal weight: 3.9990 chunk 137 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 235 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.159784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.128342 restraints weight = 105841.790| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 4.36 r_work: 0.3412 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 13758 Z= 0.157 Angle : 0.516 5.993 18678 Z= 0.250 Chirality : 0.044 0.144 2052 Planarity : 0.004 0.060 2436 Dihedral : 6.166 58.520 1948 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.66 % Favored : 96.28 % Rotamer: Outliers : 0.84 % Allowed : 15.91 % Favored : 83.25 % 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: -0.74 (0.21), residues: 1708 helix: -0.06 (0.28), residues: 416 sheet: -0.28 (0.34), residues: 196 loop : -0.68 (0.19), residues: 1096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 284 HIS 0.002 0.000 HIS A 9 PHE 0.013 0.001 PHE D 51 TYR 0.019 0.001 TYR B 75 ARG 0.007 0.000 ARG C 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6212.31 seconds wall clock time: 110 minutes 56.22 seconds (6656.22 seconds total)