Starting phenix.real_space_refine on Tue Feb 20 02:33:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8u_4761/02_2024/6r8u_4761_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8u_4761/02_2024/6r8u_4761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8u_4761/02_2024/6r8u_4761.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8u_4761/02_2024/6r8u_4761.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8u_4761/02_2024/6r8u_4761_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6r8u_4761/02_2024/6r8u_4761_trim_updated.pdb" } resolution = 3.0 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= 0.136 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 88 5.16 5 C 8524 2.51 5 N 2420 2.21 5 O 2500 1.98 5 H 13176 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 ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 134": "OE1" <-> "OE2" Residue "A GLU 158": "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 GLU 370": "OE1" <-> "OE2" Residue "A ARG 375": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A GLU 392": "OE1" <-> "OE2" Residue "A GLU 401": "OE1" <-> "OE2" Residue "A ARG 431": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "B TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 GLU 225": "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 ARG 107": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "D TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 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 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 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: 26712 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 6655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6661 Chain: "B" Number of atoms: 6655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6661 Chain: "D" Number of atoms: 6655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6661 Chain: "C" Number of atoms: 6655 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 Conformer: "B" Number of residues, atoms: 425, 6623 Classifications: {'peptide': 425} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 21, 'TRANS': 403} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 24 bond proxies already assigned to first conformer: 6661 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: 22.02, per 1000 atoms: 0.82 Number of scatterers: 26712 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 88 16.00 P 4 15.00 O 2500 8.00 N 2420 7.00 C 8524 6.00 H 13176 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: 21.98 Conformation dependent library (CDL) restraints added in 6.1 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 20.5% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.24 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 31 through 36 removed outlier: 3.689A pdb=" N LYS A 34 " --> pdb=" O THR A 31 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP A 35 " --> pdb=" O ARG A 32 " (cutoff:3.500A) 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: 3.641A pdb=" N ALA A 57 " --> pdb=" O ILE A 54 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU A 58 " --> pdb=" O ASP A 55 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 59 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN A 60 " --> pdb=" O ALA A 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE A 62 " --> pdb=" O SER A 59 " (cutoff:3.500A) removed outlier: 4.130A 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 152 through 158 Processing helix chain 'A' and resid 220 through 231 removed outlier: 4.007A pdb=" N GLU A 225 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 229 " --> pdb=" O GLU A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 251 removed outlier: 3.552A pdb=" N ALA A 251 " --> pdb=" O LYS A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 290 removed outlier: 4.108A 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 423 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 31 through 36 removed outlier: 3.689A pdb=" N LYS B 34 " --> pdb=" O THR B 31 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP B 35 " --> pdb=" O ARG B 32 " (cutoff:3.500A) 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: 3.641A pdb=" N ALA B 57 " --> pdb=" O ILE B 54 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU B 58 " --> pdb=" O ASP B 55 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER B 59 " --> pdb=" O PHE B 56 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN B 60 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE B 62 " --> pdb=" O SER B 59 " (cutoff:3.500A) removed outlier: 4.130A 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 231 removed outlier: 4.007A pdb=" N GLU B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU B 229 " --> pdb=" O GLU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.552A pdb=" N ALA B 251 " --> pdb=" O LYS B 247 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 290 removed outlier: 4.107A 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 423 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 31 through 36 removed outlier: 3.689A pdb=" N LYS D 34 " --> pdb=" O THR D 31 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N ASP D 35 " --> pdb=" O ARG D 32 " (cutoff:3.500A) 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: 3.642A pdb=" N ALA D 57 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU D 58 " --> pdb=" O ASP D 55 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER D 59 " --> pdb=" O PHE D 56 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N ASN D 60 " --> pdb=" O ALA D 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE D 62 " --> pdb=" O SER D 59 " (cutoff:3.500A) removed outlier: 4.130A 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 152 through 158 Processing helix chain 'D' and resid 220 through 231 removed outlier: 4.007A pdb=" N GLU D 225 " --> pdb=" O ASP D 221 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU D 229 " --> pdb=" O GLU D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 244 through 251 removed outlier: 3.552A pdb=" N ALA D 251 " --> pdb=" O LYS D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 290 removed outlier: 4.107A 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 423 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 31 through 36 removed outlier: 3.688A pdb=" N LYS C 34 " --> pdb=" O THR C 31 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASP C 35 " --> pdb=" O ARG C 32 " (cutoff:3.500A) 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: 3.641A pdb=" N ALA C 57 " --> pdb=" O ILE C 54 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LEU C 58 " --> pdb=" O ASP C 55 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER C 59 " --> pdb=" O PHE C 56 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N ASN C 60 " --> pdb=" O ALA C 57 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ILE C 62 " --> pdb=" O SER C 59 " (cutoff:3.500A) removed outlier: 4.130A 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 158 Processing helix chain 'C' and resid 220 through 231 removed outlier: 4.007A pdb=" N GLU C 225 " --> pdb=" O ASP C 221 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 229 " --> pdb=" O GLU C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 251 removed outlier: 3.551A pdb=" N ALA C 251 " --> pdb=" O LYS C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 290 removed outlier: 4.108A 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: 7.256A pdb=" N SER A 20 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY A 70 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA A 22 " --> pdb=" O GLY A 70 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR A 135 " --> pdb=" O VAL A 21 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N LEU A 23 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL A 137 " --> pdb=" O LEU A 23 " (cutoff:3.500A) removed outlier: 5.067A 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 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: 6.709A pdb=" N CYS A 382 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 6.607A 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: 7.256A pdb=" N SER B 20 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY B 70 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA B 22 " --> pdb=" O GLY B 70 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR B 135 " --> pdb=" O VAL B 21 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU B 23 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N VAL B 137 " --> pdb=" O LEU B 23 " (cutoff:3.500A) removed outlier: 5.067A 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: 6.709A pdb=" N CYS B 382 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 6.607A 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: 7.255A pdb=" N SER D 20 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY D 70 " --> pdb=" O SER D 20 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA D 22 " --> pdb=" O GLY D 70 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N TYR D 135 " --> pdb=" O VAL D 21 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU D 23 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL D 137 " --> pdb=" O LEU D 23 " (cutoff:3.500A) removed outlier: 5.067A 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 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: 6.708A pdb=" N CYS D 382 " --> pdb=" O VAL D 366 " (cutoff:3.500A) removed outlier: 6.607A 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: 7.256A pdb=" N SER C 20 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N GLY C 70 " --> pdb=" O SER C 20 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N ALA C 22 " --> pdb=" O GLY C 70 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR C 135 " --> pdb=" O VAL C 21 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N LEU C 23 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL C 137 " --> pdb=" O LEU C 23 " (cutoff:3.500A) removed outlier: 5.067A 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 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: 6.708A pdb=" N CYS C 382 " --> pdb=" O VAL C 366 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL C 415 " --> pdb=" O VAL C 383 " (cutoff:3.500A) No H-bonds generated for sheet with id= X 228 hydrogen bonds defined for protein. 636 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: 10.59 Time building geometry restraints manager: 22.40 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: 13140 1.04 - 1.24: 1273 1.24 - 1.43: 4663 1.43 - 1.63: 7800 1.63 - 1.83: 140 Bond restraints: 27016 Sorted by residual: bond pdb=" C MET B 328 " pdb=" O MET B 328 " ideal model delta sigma weight residual 1.234 1.174 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" C MET C 328 " pdb=" O MET C 328 " ideal model delta sigma weight residual 1.234 1.174 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" C MET A 328 " pdb=" O MET A 328 " ideal model delta sigma weight residual 1.234 1.174 0.059 1.17e-02 7.31e+03 2.58e+01 bond pdb=" C MET D 328 " pdb=" O MET D 328 " ideal model delta sigma weight residual 1.234 1.175 0.059 1.17e-02 7.31e+03 2.53e+01 bond pdb=" C LYS B 34 " pdb=" O LYS B 34 " ideal model delta sigma weight residual 1.242 1.192 0.050 1.00e-02 1.00e+04 2.50e+01 ... (remaining 27011 not shown) Histogram of bond angle deviations from ideal: 94.20 - 102.73: 92 102.73 - 111.26: 28152 111.26 - 119.79: 10211 119.79 - 128.32: 10097 128.32 - 136.86: 152 Bond angle restraints: 48704 Sorted by residual: angle pdb=" N LEU C 36 " pdb=" CA LEU C 36 " pdb=" C LEU C 36 " ideal model delta sigma weight residual 112.54 104.08 8.46 1.22e+00 6.72e-01 4.80e+01 angle pdb=" N LEU A 36 " pdb=" CA LEU A 36 " pdb=" C LEU A 36 " ideal model delta sigma weight residual 112.54 104.09 8.45 1.22e+00 6.72e-01 4.80e+01 angle pdb=" N LEU B 36 " pdb=" CA LEU B 36 " pdb=" C LEU B 36 " ideal model delta sigma weight residual 112.54 104.13 8.41 1.22e+00 6.72e-01 4.75e+01 angle pdb=" N LEU D 36 " pdb=" CA LEU D 36 " pdb=" C LEU D 36 " ideal model delta sigma weight residual 112.54 104.13 8.41 1.22e+00 6.72e-01 4.75e+01 angle pdb=" N GLU D 229 " pdb=" CA GLU D 229 " pdb=" C GLU D 229 " ideal model delta sigma weight residual 113.28 107.15 6.13 1.22e+00 6.72e-01 2.53e+01 ... (remaining 48699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.80: 11908 24.80 - 49.60: 692 49.60 - 74.40: 144 74.40 - 99.20: 4 99.20 - 124.00: 4 Dihedral angle restraints: 12752 sinusoidal: 6976 harmonic: 5776 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 64.00 -124.00 1 2.00e+01 2.50e-03 3.74e+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 63.95 -123.95 1 2.00e+01 2.50e-03 3.74e+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 -173.46 113.46 1 2.00e+01 2.50e-03 3.36e+01 ... (remaining 12749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1592 0.089 - 0.177: 416 0.177 - 0.266: 32 0.266 - 0.355: 4 0.355 - 0.444: 8 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CA VAL D 277 " pdb=" N VAL D 277 " pdb=" C VAL D 277 " pdb=" CB VAL D 277 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA VAL A 277 " pdb=" N VAL A 277 " pdb=" C VAL A 277 " pdb=" CB VAL A 277 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.91e+00 chirality pdb=" CA VAL C 277 " pdb=" N VAL C 277 " pdb=" C VAL C 277 " pdb=" CB VAL C 277 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.91e+00 ... (remaining 2049 not shown) Planarity restraints: 4072 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 88 " -0.019 2.00e-02 2.50e+03 3.12e-02 3.89e+01 pdb=" CG TRP C 88 " 0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP C 88 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP C 88 " -0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP C 88 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP C 88 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 88 " 0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 88 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 88 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP C 88 " 0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP C 88 " -0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP C 88 " 0.009 2.00e-02 2.50e+03 pdb=" HE3 TRP C 88 " 0.073 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 88 " -0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 88 " -0.078 2.00e-02 2.50e+03 pdb=" HH2 TRP C 88 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 88 " 0.020 2.00e-02 2.50e+03 3.12e-02 3.88e+01 pdb=" CG TRP B 88 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP B 88 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B 88 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP B 88 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP B 88 " -0.009 2.00e-02 2.50e+03 pdb=" CE3 TRP B 88 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 88 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 88 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP B 88 " -0.010 2.00e-02 2.50e+03 pdb=" HD1 TRP B 88 " 0.016 2.00e-02 2.50e+03 pdb=" HE1 TRP B 88 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP B 88 " -0.074 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 88 " 0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 88 " 0.078 2.00e-02 2.50e+03 pdb=" HH2 TRP B 88 " -0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 88 " 0.020 2.00e-02 2.50e+03 3.12e-02 3.88e+01 pdb=" CG TRP D 88 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TRP D 88 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP D 88 " 0.018 2.00e-02 2.50e+03 pdb=" NE1 TRP D 88 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP D 88 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP D 88 " -0.020 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 88 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 88 " 0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP D 88 " -0.009 2.00e-02 2.50e+03 pdb=" HD1 TRP D 88 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 TRP D 88 " -0.008 2.00e-02 2.50e+03 pdb=" HE3 TRP D 88 " -0.074 2.00e-02 2.50e+03 pdb=" HZ2 TRP D 88 " 0.015 2.00e-02 2.50e+03 pdb=" HZ3 TRP D 88 " 0.077 2.00e-02 2.50e+03 pdb=" HH2 TRP D 88 " -0.040 2.00e-02 2.50e+03 ... (remaining 4069 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1558 2.18 - 2.79: 53160 2.79 - 3.39: 71732 3.39 - 4.00: 101863 4.00 - 4.60: 155765 Nonbonded interactions: 384078 Sorted by model distance: nonbonded pdb=" HE1 TYR B 145 " pdb=" HH TYR B 149 " model vdw 1.576 2.100 nonbonded pdb=" HE1 TYR D 145 " pdb=" HH TYR D 149 " model vdw 1.577 2.100 nonbonded pdb=" HE1 TYR A 145 " pdb=" HH TYR A 149 " model vdw 1.577 2.100 nonbonded pdb=" HE1 TYR C 145 " pdb=" HH TYR C 149 " model vdw 1.577 2.100 nonbonded pdb=" OD1 ASP B 276 " pdb=" H ASP B 276 " model vdw 1.651 1.850 ... (remaining 384073 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 150 or resid 152 through 219 or resid 222 throug \ h 431 or resid 501)) selection = (chain 'B' and (resid 7 through 150 or resid 152 through 219 or resid 222 throug \ h 431 or resid 501)) selection = (chain 'C' and (resid 7 through 150 or resid 152 through 219 or resid 222 throug \ h 431 or resid 501)) selection = (chain 'D' and (resid 7 through 150 or resid 152 through 219 or resid 222 throug \ h 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: 0.500 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: 0.450 Extract box with map and model: 3.510 Check model and map are aligned: 0.450 Set scattering table: 0.270 Process input model: 102.470 Find NCS groups from input model: 1.470 Set up NCS constraints: 0.150 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:13.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 122.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6384 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 : 0.011 0.069 13840 Z= 0.767 Angle : 1.282 10.360 18776 Z= 0.785 Chirality : 0.078 0.444 2052 Planarity : 0.011 0.092 2448 Dihedral : 15.140 124.001 5188 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.57 % Favored : 91.43 % Rotamer: Outliers : 3.60 % Allowed : 9.14 % Favored : 87.26 % Cbeta Deviations : 0.25 % 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: -3.30 (0.17), residues: 1708 helix: -3.76 (0.16), residues: 384 sheet: -1.79 (0.36), residues: 184 loop : -1.75 (0.16), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.008 TRP D 284 HIS 0.017 0.006 HIS C 143 PHE 0.033 0.005 PHE C 259 TYR 0.020 0.006 TYR C 222 ARG 0.039 0.005 ARG C 107 *********************** 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 351 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 303 time to evaluate : 2.424 Fit side-chains REVERT: A 39 LYS cc_start: 0.8089 (mttt) cc_final: 0.7538 (mtmt) REVERT: A 115 ARG cc_start: 0.6426 (mpt180) cc_final: 0.6204 (mmt180) REVERT: A 123 GLN cc_start: 0.7686 (OUTLIER) cc_final: 0.7252 (mm-40) REVERT: A 148 ASP cc_start: 0.7818 (t0) cc_final: 0.7606 (t0) REVERT: A 186 ASN cc_start: 0.7395 (m-40) cc_final: 0.7119 (m-40) REVERT: A 191 GLU cc_start: 0.7512 (mm-30) cc_final: 0.7175 (mm-30) REVERT: A 198 ASN cc_start: 0.8102 (t0) cc_final: 0.7888 (p0) REVERT: A 229 GLU cc_start: 0.8369 (tt0) cc_final: 0.8105 (tt0) REVERT: A 232 ARG cc_start: 0.7851 (mtt90) cc_final: 0.7387 (mtm-85) REVERT: A 237 SER cc_start: 0.9001 (m) cc_final: 0.8767 (p) REVERT: A 328 MET cc_start: 0.7314 (OUTLIER) cc_final: 0.7004 (mtp) REVERT: A 355 ARG cc_start: 0.6686 (mmt90) cc_final: 0.5804 (tpt-90) REVERT: A 380 ARG cc_start: 0.6971 (ttp-170) cc_final: 0.6488 (mtp85) REVERT: A 406 ARG cc_start: 0.7510 (OUTLIER) cc_final: 0.6896 (mtt180) REVERT: A 428 LYS cc_start: 0.8165 (tttt) cc_final: 0.7857 (mtpp) REVERT: B 11 MET cc_start: 0.8189 (mmm) cc_final: 0.7918 (tpp) REVERT: B 39 LYS cc_start: 0.8101 (mttt) cc_final: 0.7566 (mtmt) REVERT: B 92 ASN cc_start: 0.7427 (m-40) cc_final: 0.7178 (m-40) REVERT: B 123 GLN cc_start: 0.7761 (OUTLIER) cc_final: 0.7321 (mm-40) REVERT: B 148 ASP cc_start: 0.7859 (t0) cc_final: 0.7621 (t0) REVERT: B 186 ASN cc_start: 0.7405 (m-40) cc_final: 0.7193 (m110) REVERT: B 191 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7183 (mm-30) REVERT: B 198 ASN cc_start: 0.8061 (t0) cc_final: 0.7846 (p0) REVERT: B 229 GLU cc_start: 0.8375 (tt0) cc_final: 0.8145 (tt0) REVERT: B 232 ARG cc_start: 0.7787 (mtt90) cc_final: 0.7424 (mtm-85) REVERT: B 237 SER cc_start: 0.9009 (m) cc_final: 0.8773 (p) REVERT: B 311 GLU cc_start: 0.8290 (tt0) cc_final: 0.8082 (tt0) REVERT: B 355 ARG cc_start: 0.6777 (mmt90) cc_final: 0.5880 (tpt-90) REVERT: B 380 ARG cc_start: 0.7088 (ttp-170) cc_final: 0.6623 (mtp85) REVERT: B 406 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.6873 (mtp180) REVERT: B 428 LYS cc_start: 0.8315 (tttt) cc_final: 0.7928 (mtpp) REVERT: D 11 MET cc_start: 0.8117 (mmm) cc_final: 0.7814 (tpp) REVERT: D 39 LYS cc_start: 0.8170 (mttt) cc_final: 0.7626 (mtmt) REVERT: D 115 ARG cc_start: 0.6436 (mpt180) cc_final: 0.6119 (mmt180) REVERT: D 123 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.6020 (mp10) REVERT: D 148 ASP cc_start: 0.7843 (t0) cc_final: 0.7614 (t0) REVERT: D 186 ASN cc_start: 0.7408 (m-40) cc_final: 0.7141 (m-40) REVERT: D 191 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7161 (mm-30) REVERT: D 229 GLU cc_start: 0.8327 (tt0) cc_final: 0.8105 (tt0) REVERT: D 232 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7382 (mtm-85) REVERT: D 237 SER cc_start: 0.8999 (m) cc_final: 0.8755 (p) REVERT: D 311 GLU cc_start: 0.8304 (tt0) cc_final: 0.8088 (tt0) REVERT: D 328 MET cc_start: 0.7421 (OUTLIER) cc_final: 0.7147 (mtp) REVERT: D 355 ARG cc_start: 0.6784 (mmt90) cc_final: 0.5884 (tpt-90) REVERT: D 380 ARG cc_start: 0.7058 (ttp-170) cc_final: 0.6583 (mtp85) REVERT: D 406 ARG cc_start: 0.7548 (OUTLIER) cc_final: 0.6931 (mtp180) REVERT: D 428 LYS cc_start: 0.8315 (tttt) cc_final: 0.7956 (mtpp) REVERT: C 11 MET cc_start: 0.8176 (mmm) cc_final: 0.7959 (tpp) REVERT: C 39 LYS cc_start: 0.8195 (mttt) cc_final: 0.7657 (mtmt) REVERT: C 123 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7322 (mm-40) REVERT: C 148 ASP cc_start: 0.7814 (t0) cc_final: 0.7585 (t0) REVERT: C 186 ASN cc_start: 0.7428 (m-40) cc_final: 0.7202 (m110) REVERT: C 191 GLU cc_start: 0.7446 (mm-30) cc_final: 0.7150 (mm-30) REVERT: C 229 GLU cc_start: 0.8390 (tt0) cc_final: 0.8159 (tt0) REVERT: C 232 ARG cc_start: 0.7825 (mtt90) cc_final: 0.7393 (mtm-85) REVERT: C 237 SER cc_start: 0.8993 (m) cc_final: 0.8766 (p) REVERT: C 311 GLU cc_start: 0.8326 (tt0) cc_final: 0.8083 (tt0) REVERT: C 355 ARG cc_start: 0.6781 (mmt90) cc_final: 0.5877 (tpt-90) REVERT: C 380 ARG cc_start: 0.6980 (ttp-170) cc_final: 0.6498 (mtp85) REVERT: C 406 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.6929 (mtp180) REVERT: C 428 LYS cc_start: 0.8326 (tttt) cc_final: 0.7932 (mtpp) outliers start: 48 outliers final: 8 residues processed: 327 average time/residue: 2.9161 time to fit residues: 1037.6502 Evaluate side-chains 232 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 214 time to evaluate : 2.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 406 ARG Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 328 MET Chi-restraints excluded: chain D residue 406 ARG Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 406 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.0570 chunk 127 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 85 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 152 optimal weight: 0.1980 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 147 GLN A 235 ASN A 310 ASN A 429 GLN B 106 GLN B 147 GLN B 235 ASN B 310 ASN D 106 GLN D 147 GLN D 235 ASN D 310 ASN C 106 GLN C 147 GLN C 235 ASN C 310 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.1615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13840 Z= 0.172 Angle : 0.625 6.042 18776 Z= 0.319 Chirality : 0.046 0.152 2052 Planarity : 0.005 0.044 2448 Dihedral : 8.840 88.068 1994 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 3.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.94 % Allowed : 16.62 % Favored : 81.44 % 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: -2.43 (0.18), residues: 1708 helix: -2.30 (0.22), residues: 392 sheet: -1.59 (0.35), residues: 192 loop : -1.38 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 284 HIS 0.012 0.001 HIS A 257 PHE 0.014 0.001 PHE D 259 TYR 0.014 0.001 TYR A 114 ARG 0.006 0.001 ARG A 115 *********************** 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 258 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 234 time to evaluate : 2.198 Fit side-chains revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8180 (mttt) cc_final: 0.7624 (mtmt) REVERT: A 106 GLN cc_start: 0.6384 (OUTLIER) cc_final: 0.5304 (mp-120) REVERT: A 115 ARG cc_start: 0.6530 (mpt180) cc_final: 0.6198 (mmt-90) REVERT: A 123 GLN cc_start: 0.7376 (OUTLIER) cc_final: 0.6659 (mt0) REVERT: A 126 ASP cc_start: 0.6969 (OUTLIER) cc_final: 0.6421 (p0) REVERT: A 134 GLU cc_start: 0.7712 (mt-10) cc_final: 0.6898 (tt0) REVERT: A 155 ASP cc_start: 0.7821 (t70) cc_final: 0.6825 (t0) REVERT: A 186 ASN cc_start: 0.7262 (m-40) cc_final: 0.6983 (m-40) REVERT: A 191 GLU cc_start: 0.7274 (OUTLIER) cc_final: 0.7017 (mm-30) REVERT: A 198 ASN cc_start: 0.8072 (t0) cc_final: 0.7872 (p0) REVERT: A 228 GLU cc_start: 0.7713 (mt-10) cc_final: 0.7485 (mt-10) REVERT: A 229 GLU cc_start: 0.8163 (tt0) cc_final: 0.7857 (tt0) REVERT: A 237 SER cc_start: 0.8954 (m) cc_final: 0.8737 (p) REVERT: A 243 ASP cc_start: 0.5818 (m-30) cc_final: 0.5212 (m-30) REVERT: A 279 THR cc_start: 0.8016 (p) cc_final: 0.7708 (t) REVERT: A 355 ARG cc_start: 0.6791 (mmt90) cc_final: 0.5931 (tpt-90) REVERT: A 380 ARG cc_start: 0.7029 (ttp-170) cc_final: 0.6569 (mtp85) REVERT: A 428 LYS cc_start: 0.8254 (tttt) cc_final: 0.7883 (mtpp) REVERT: B 11 MET cc_start: 0.7887 (mmm) cc_final: 0.7644 (tpp) REVERT: B 39 LYS cc_start: 0.8114 (mttt) cc_final: 0.7579 (mtmt) REVERT: B 106 GLN cc_start: 0.6466 (OUTLIER) cc_final: 0.5255 (mp-120) REVERT: B 115 ARG cc_start: 0.6504 (mmt90) cc_final: 0.6235 (mmt-90) REVERT: B 123 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.6861 (mt0) REVERT: B 134 GLU cc_start: 0.7602 (mt-10) cc_final: 0.6962 (tt0) REVERT: B 155 ASP cc_start: 0.7811 (t70) cc_final: 0.6779 (t0) REVERT: B 198 ASN cc_start: 0.8031 (t0) cc_final: 0.7830 (p0) REVERT: B 228 GLU cc_start: 0.7819 (mt-10) cc_final: 0.7548 (mt-10) REVERT: B 229 GLU cc_start: 0.8155 (tt0) cc_final: 0.7892 (tt0) REVERT: B 243 ASP cc_start: 0.5832 (m-30) cc_final: 0.5580 (m-30) REVERT: B 279 THR cc_start: 0.7971 (p) cc_final: 0.7641 (t) REVERT: B 355 ARG cc_start: 0.6824 (mmt90) cc_final: 0.5917 (tpt-90) REVERT: B 375 ARG cc_start: 0.7028 (mtm110) cc_final: 0.6386 (ttm110) REVERT: B 380 ARG cc_start: 0.7072 (ttp-170) cc_final: 0.6630 (mtp85) REVERT: B 428 LYS cc_start: 0.8145 (tttt) cc_final: 0.7789 (mtpp) REVERT: D 11 MET cc_start: 0.8025 (mmm) cc_final: 0.7789 (tpp) REVERT: D 39 LYS cc_start: 0.8173 (mttt) cc_final: 0.7616 (mtmt) REVERT: D 106 GLN cc_start: 0.6407 (OUTLIER) cc_final: 0.5319 (mp-120) REVERT: D 115 ARG cc_start: 0.6535 (mpt180) cc_final: 0.6131 (mmt-90) REVERT: D 123 GLN cc_start: 0.7474 (OUTLIER) cc_final: 0.6684 (mt0) REVERT: D 126 ASP cc_start: 0.6955 (OUTLIER) cc_final: 0.6408 (p0) REVERT: D 134 GLU cc_start: 0.7706 (mt-10) cc_final: 0.7008 (tt0) REVERT: D 155 ASP cc_start: 0.7881 (t70) cc_final: 0.6829 (t0) REVERT: D 186 ASN cc_start: 0.7265 (m-40) cc_final: 0.6996 (m-40) REVERT: D 191 GLU cc_start: 0.7254 (OUTLIER) cc_final: 0.7033 (mm-30) REVERT: D 228 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7442 (mt-10) REVERT: D 229 GLU cc_start: 0.8140 (tt0) cc_final: 0.7834 (tt0) REVERT: D 237 SER cc_start: 0.8880 (m) cc_final: 0.8590 (p) REVERT: D 243 ASP cc_start: 0.5668 (m-30) cc_final: 0.5057 (m-30) REVERT: D 279 THR cc_start: 0.7933 (p) cc_final: 0.7640 (t) REVERT: D 355 ARG cc_start: 0.6806 (mmt90) cc_final: 0.5925 (tpt-90) REVERT: D 375 ARG cc_start: 0.7034 (mtm110) cc_final: 0.6418 (ttm110) REVERT: D 380 ARG cc_start: 0.7054 (ttp-170) cc_final: 0.6562 (mtp85) REVERT: D 428 LYS cc_start: 0.8161 (tttt) cc_final: 0.7797 (mtpp) REVERT: C 39 LYS cc_start: 0.8182 (mttt) cc_final: 0.7632 (mtmt) REVERT: C 106 GLN cc_start: 0.6380 (OUTLIER) cc_final: 0.5226 (mp-120) REVERT: C 115 ARG cc_start: 0.6544 (mmt90) cc_final: 0.6313 (mmt-90) REVERT: C 123 GLN cc_start: 0.7271 (OUTLIER) cc_final: 0.6599 (mt0) REVERT: C 126 ASP cc_start: 0.6958 (OUTLIER) cc_final: 0.6387 (p0) REVERT: C 134 GLU cc_start: 0.7587 (mt-10) cc_final: 0.6935 (tt0) REVERT: C 155 ASP cc_start: 0.7804 (t70) cc_final: 0.6811 (t0) REVERT: C 228 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7583 (mt-10) REVERT: C 229 GLU cc_start: 0.8179 (tt0) cc_final: 0.7872 (tt0) REVERT: C 237 SER cc_start: 0.8968 (m) cc_final: 0.8744 (p) REVERT: C 243 ASP cc_start: 0.5830 (m-30) cc_final: 0.5224 (m-30) REVERT: C 279 THR cc_start: 0.8025 (p) cc_final: 0.7700 (t) REVERT: C 355 ARG cc_start: 0.6798 (mmt90) cc_final: 0.5919 (tpt-90) REVERT: C 375 ARG cc_start: 0.7029 (mtm110) cc_final: 0.6396 (ttm110) REVERT: C 380 ARG cc_start: 0.6969 (ttp-170) cc_final: 0.6494 (mtp85) REVERT: C 428 LYS cc_start: 0.8165 (tttt) cc_final: 0.7796 (mtpp) outliers start: 24 outliers final: 8 residues processed: 246 average time/residue: 3.1207 time to fit residues: 832.7014 Evaluate side-chains 228 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 207 time to evaluate : 2.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 106 GLN Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 106 GLN Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 154 ILE Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 106 GLN Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 191 GLU Chi-restraints excluded: chain D residue 230 ASP Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 106 GLN Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 154 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 126 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 165 optimal weight: 4.9990 chunk 136 optimal weight: 9.9990 chunk 151 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN A 347 GLN A 399 ASN B 310 ASN B 347 GLN B 399 ASN D 310 ASN D 347 GLN D 399 ASN C 310 ASN C 347 GLN C 399 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 13840 Z= 0.375 Angle : 0.611 5.855 18776 Z= 0.312 Chirality : 0.049 0.155 2052 Planarity : 0.005 0.040 2448 Dihedral : 7.846 75.705 1964 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 1.87 % Allowed : 17.24 % Favored : 80.89 % 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: -2.00 (0.19), residues: 1708 helix: -1.74 (0.26), residues: 392 sheet: -1.10 (0.37), residues: 192 loop : -1.23 (0.17), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 284 HIS 0.008 0.001 HIS A 257 PHE 0.012 0.001 PHE D 259 TYR 0.010 0.001 TYR C 309 ARG 0.003 0.000 ARG B 162 *********************** 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 233 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 210 time to evaluate : 2.503 Fit side-chains REVERT: A 39 LYS cc_start: 0.8210 (mttt) cc_final: 0.7626 (mtmt) REVERT: A 115 ARG cc_start: 0.6523 (mpt180) cc_final: 0.6271 (mmt90) REVERT: A 123 GLN cc_start: 0.7597 (OUTLIER) cc_final: 0.5689 (mp10) REVERT: A 126 ASP cc_start: 0.6993 (OUTLIER) cc_final: 0.6456 (p0) REVERT: A 134 GLU cc_start: 0.7671 (mt-10) cc_final: 0.7030 (tt0) REVERT: A 155 ASP cc_start: 0.8061 (t70) cc_final: 0.7030 (t0) REVERT: A 186 ASN cc_start: 0.7226 (m-40) cc_final: 0.6916 (m-40) REVERT: A 198 ASN cc_start: 0.8061 (t0) cc_final: 0.7860 (p0) REVERT: A 229 GLU cc_start: 0.8108 (tt0) cc_final: 0.7833 (tt0) REVERT: A 243 ASP cc_start: 0.5897 (m-30) cc_final: 0.5662 (m-30) REVERT: A 279 THR cc_start: 0.7841 (p) cc_final: 0.7515 (t) REVERT: A 355 ARG cc_start: 0.6749 (mmt90) cc_final: 0.5887 (tpt90) REVERT: A 380 ARG cc_start: 0.7082 (ttp-170) cc_final: 0.6621 (mtp85) REVERT: A 428 LYS cc_start: 0.8282 (tttt) cc_final: 0.7921 (mtpp) REVERT: B 11 MET cc_start: 0.7838 (mmm) cc_final: 0.7484 (tpp) REVERT: B 39 LYS cc_start: 0.8237 (mttt) cc_final: 0.7641 (mtmt) REVERT: B 123 GLN cc_start: 0.7475 (OUTLIER) cc_final: 0.5656 (mp10) REVERT: B 126 ASP cc_start: 0.7042 (m-30) cc_final: 0.6438 (p0) REVERT: B 134 GLU cc_start: 0.7668 (mt-10) cc_final: 0.6933 (tt0) REVERT: B 155 ASP cc_start: 0.7951 (t70) cc_final: 0.6882 (t0) REVERT: B 198 ASN cc_start: 0.8082 (t0) cc_final: 0.7817 (p0) REVERT: B 229 GLU cc_start: 0.8086 (tt0) cc_final: 0.7814 (tt0) REVERT: B 243 ASP cc_start: 0.5872 (m-30) cc_final: 0.5612 (m-30) REVERT: B 267 ASP cc_start: 0.6341 (p0) cc_final: 0.6053 (p0) REVERT: B 279 THR cc_start: 0.7800 (p) cc_final: 0.7476 (t) REVERT: B 311 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: B 355 ARG cc_start: 0.6745 (mmt90) cc_final: 0.5860 (tpt90) REVERT: B 380 ARG cc_start: 0.7091 (ttp-170) cc_final: 0.6624 (mtp85) REVERT: B 428 LYS cc_start: 0.8239 (tttt) cc_final: 0.7880 (mtpp) REVERT: D 11 MET cc_start: 0.7852 (mmm) cc_final: 0.7582 (tpp) REVERT: D 39 LYS cc_start: 0.8198 (mttt) cc_final: 0.7615 (mtmt) REVERT: D 115 ARG cc_start: 0.6548 (mpt180) cc_final: 0.6323 (mmt90) REVERT: D 123 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.5683 (mp10) REVERT: D 126 ASP cc_start: 0.6991 (OUTLIER) cc_final: 0.6460 (p0) REVERT: D 134 GLU cc_start: 0.7698 (mt-10) cc_final: 0.7043 (tt0) REVERT: D 155 ASP cc_start: 0.8034 (t70) cc_final: 0.6986 (t0) REVERT: D 229 GLU cc_start: 0.8065 (tt0) cc_final: 0.7815 (tt0) REVERT: D 355 ARG cc_start: 0.6767 (mmt90) cc_final: 0.5867 (tpt90) REVERT: D 380 ARG cc_start: 0.7110 (ttp-170) cc_final: 0.6642 (mtp85) REVERT: D 428 LYS cc_start: 0.8223 (tttt) cc_final: 0.7871 (mtpp) REVERT: C 11 MET cc_start: 0.7893 (mmm) cc_final: 0.7653 (mmm) REVERT: C 39 LYS cc_start: 0.8218 (mttt) cc_final: 0.7631 (mtmt) REVERT: C 123 GLN cc_start: 0.7398 (OUTLIER) cc_final: 0.5568 (mp10) REVERT: C 126 ASP cc_start: 0.6932 (OUTLIER) cc_final: 0.6362 (p0) REVERT: C 134 GLU cc_start: 0.7665 (mt-10) cc_final: 0.6908 (tt0) REVERT: C 155 ASP cc_start: 0.7937 (t70) cc_final: 0.6811 (t0) REVERT: C 229 GLU cc_start: 0.8205 (tt0) cc_final: 0.7931 (tt0) REVERT: C 243 ASP cc_start: 0.5944 (m-30) cc_final: 0.5669 (m-30) REVERT: C 267 ASP cc_start: 0.6292 (p0) cc_final: 0.6011 (p0) REVERT: C 279 THR cc_start: 0.7879 (p) cc_final: 0.7557 (t) REVERT: C 355 ARG cc_start: 0.6765 (mmt90) cc_final: 0.5885 (tpt90) REVERT: C 375 ARG cc_start: 0.7013 (mtm110) cc_final: 0.6680 (ttm-80) REVERT: C 380 ARG cc_start: 0.7075 (ttp-170) cc_final: 0.6578 (mtp85) REVERT: C 428 LYS cc_start: 0.8229 (tttt) cc_final: 0.7872 (mtpp) outliers start: 23 outliers final: 7 residues processed: 223 average time/residue: 2.9872 time to fit residues: 725.5011 Evaluate side-chains 210 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 195 time to evaluate : 2.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASP Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 35 ASP Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 311 GLU Chi-restraints excluded: chain D residue 35 ASP Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 126 ASP Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 126 ASP Chi-restraints excluded: chain C residue 321 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 153 optimal weight: 3.9990 chunk 162 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 145 optimal weight: 0.0070 chunk 43 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 310 ASN D 310 ASN C 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 13840 Z= 0.169 Angle : 0.547 5.945 18776 Z= 0.272 Chirality : 0.045 0.148 2052 Planarity : 0.004 0.034 2448 Dihedral : 7.205 58.998 1964 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.76 % Allowed : 18.77 % Favored : 80.47 % 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: -1.65 (0.20), residues: 1708 helix: -1.38 (0.27), residues: 392 sheet: -0.86 (0.36), residues: 208 loop : -1.03 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 284 HIS 0.007 0.001 HIS D 257 PHE 0.006 0.001 PHE B 178 TYR 0.007 0.001 TYR C 309 ARG 0.003 0.000 ARG B 162 *********************** 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 217 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 210 time to evaluate : 2.196 Fit side-chains REVERT: A 39 LYS cc_start: 0.8259 (mttt) cc_final: 0.7646 (mtmt) REVERT: A 115 ARG cc_start: 0.6568 (mpt180) cc_final: 0.6325 (mmt90) REVERT: A 123 GLN cc_start: 0.7458 (OUTLIER) cc_final: 0.5526 (mp10) REVERT: A 126 ASP cc_start: 0.6948 (m-30) cc_final: 0.6374 (p0) REVERT: A 134 GLU cc_start: 0.7685 (mt-10) cc_final: 0.6982 (tt0) REVERT: A 155 ASP cc_start: 0.8023 (t70) cc_final: 0.6951 (t0) REVERT: A 186 ASN cc_start: 0.7247 (m-40) cc_final: 0.7027 (m110) REVERT: A 198 ASN cc_start: 0.8067 (t0) cc_final: 0.7825 (p0) REVERT: A 228 GLU cc_start: 0.7561 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 229 GLU cc_start: 0.8099 (tt0) cc_final: 0.7850 (tt0) REVERT: A 243 ASP cc_start: 0.5822 (m-30) cc_final: 0.5605 (m-30) REVERT: A 267 ASP cc_start: 0.6202 (p0) cc_final: 0.5919 (p0) REVERT: A 328 MET cc_start: 0.5949 (mtp) cc_final: 0.5563 (mmt) REVERT: A 355 ARG cc_start: 0.6666 (mmt90) cc_final: 0.5790 (tpt90) REVERT: A 380 ARG cc_start: 0.7070 (ttp-170) cc_final: 0.6615 (mtp85) REVERT: A 428 LYS cc_start: 0.8268 (tttt) cc_final: 0.7892 (mtpp) REVERT: B 11 MET cc_start: 0.7732 (mmm) cc_final: 0.7470 (tpp) REVERT: B 39 LYS cc_start: 0.8219 (mttt) cc_final: 0.7613 (mtmt) REVERT: B 123 GLN cc_start: 0.7367 (OUTLIER) cc_final: 0.5533 (mp10) REVERT: B 126 ASP cc_start: 0.6969 (m-30) cc_final: 0.6375 (p0) REVERT: B 134 GLU cc_start: 0.7688 (mt-10) cc_final: 0.6961 (tt0) REVERT: B 148 ASP cc_start: 0.7236 (t0) cc_final: 0.6995 (t0) REVERT: B 155 ASP cc_start: 0.7963 (t70) cc_final: 0.6754 (t0) REVERT: B 186 ASN cc_start: 0.7203 (m-40) cc_final: 0.6978 (m110) REVERT: B 198 ASN cc_start: 0.8072 (t0) cc_final: 0.7811 (p0) REVERT: B 213 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8364 (mtm) REVERT: B 228 GLU cc_start: 0.7585 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 229 GLU cc_start: 0.8101 (tt0) cc_final: 0.7845 (tt0) REVERT: B 243 ASP cc_start: 0.5827 (m-30) cc_final: 0.5607 (m-30) REVERT: B 267 ASP cc_start: 0.6216 (p0) cc_final: 0.5931 (p0) REVERT: B 328 MET cc_start: 0.6538 (mtp) cc_final: 0.6162 (mtm) REVERT: B 355 ARG cc_start: 0.6695 (mmt90) cc_final: 0.5846 (tpt90) REVERT: B 380 ARG cc_start: 0.7082 (ttp-170) cc_final: 0.6612 (mtp85) REVERT: B 428 LYS cc_start: 0.8212 (tttt) cc_final: 0.7848 (mtpp) REVERT: D 11 MET cc_start: 0.7825 (mmm) cc_final: 0.7622 (tpp) REVERT: D 39 LYS cc_start: 0.8245 (mttt) cc_final: 0.7640 (mtmt) REVERT: D 115 ARG cc_start: 0.6608 (mpt180) cc_final: 0.6365 (mmt90) REVERT: D 123 GLN cc_start: 0.7457 (OUTLIER) cc_final: 0.5500 (mp10) REVERT: D 126 ASP cc_start: 0.6974 (m-30) cc_final: 0.6416 (p0) REVERT: D 134 GLU cc_start: 0.7684 (mt-10) cc_final: 0.7056 (tt0) REVERT: D 155 ASP cc_start: 0.8027 (t70) cc_final: 0.6988 (t0) REVERT: D 186 ASN cc_start: 0.7182 (m-40) cc_final: 0.6962 (m110) REVERT: D 228 GLU cc_start: 0.7542 (mt-10) cc_final: 0.7262 (mt-10) REVERT: D 229 GLU cc_start: 0.8118 (tt0) cc_final: 0.7843 (tt0) REVERT: D 267 ASP cc_start: 0.6281 (p0) cc_final: 0.5989 (p0) REVERT: D 328 MET cc_start: 0.5948 (mtp) cc_final: 0.5427 (mmt) REVERT: D 355 ARG cc_start: 0.6706 (mmt90) cc_final: 0.5860 (tpt90) REVERT: D 380 ARG cc_start: 0.7117 (ttp-170) cc_final: 0.6643 (mtp85) REVERT: D 428 LYS cc_start: 0.8219 (tttt) cc_final: 0.7850 (mtpp) REVERT: C 11 MET cc_start: 0.7912 (mmm) cc_final: 0.7552 (mmm) REVERT: C 39 LYS cc_start: 0.8241 (mttt) cc_final: 0.7620 (mtmt) REVERT: C 123 GLN cc_start: 0.7365 (OUTLIER) cc_final: 0.5539 (mp10) REVERT: C 126 ASP cc_start: 0.6944 (m-30) cc_final: 0.6365 (p0) REVERT: C 134 GLU cc_start: 0.7705 (mt-10) cc_final: 0.6913 (tt0) REVERT: C 155 ASP cc_start: 0.8002 (t70) cc_final: 0.6844 (t0) REVERT: C 228 GLU cc_start: 0.7583 (mt-10) cc_final: 0.7302 (mt-10) REVERT: C 229 GLU cc_start: 0.8115 (tt0) cc_final: 0.7867 (tt0) REVERT: C 243 ASP cc_start: 0.5823 (m-30) cc_final: 0.5603 (m-30) REVERT: C 267 ASP cc_start: 0.6154 (p0) cc_final: 0.5876 (p0) REVERT: C 328 MET cc_start: 0.6519 (mtp) cc_final: 0.6161 (mtm) REVERT: C 355 ARG cc_start: 0.6701 (mmt90) cc_final: 0.5852 (tpt90) REVERT: C 380 ARG cc_start: 0.7081 (ttp-170) cc_final: 0.6610 (mtp85) REVERT: C 428 LYS cc_start: 0.8226 (tttt) cc_final: 0.7872 (mtpp) outliers start: 7 outliers final: 0 residues processed: 215 average time/residue: 2.9556 time to fit residues: 694.4454 Evaluate side-chains 200 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 195 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 213 MET Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain C residue 123 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 3.9990 chunk 92 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 138 optimal weight: 1.9990 chunk 112 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 145 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 310 ASN B 235 ASN B 310 ASN D 310 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6412 moved from start: 0.2611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.035 13840 Z= 0.396 Angle : 0.579 5.882 18776 Z= 0.292 Chirality : 0.048 0.140 2052 Planarity : 0.004 0.037 2448 Dihedral : 7.256 62.007 1956 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 0.97 % Allowed : 19.46 % Favored : 79.57 % 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: -1.46 (0.26), residues: 392 sheet: -0.68 (0.37), residues: 208 loop : -1.04 (0.18), residues: 1108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 284 HIS 0.005 0.001 HIS A 257 PHE 0.008 0.002 PHE D 259 TYR 0.011 0.001 TYR D 309 ARG 0.004 0.000 ARG B 162 *********************** 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 218 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 1.943 Fit side-chains REVERT: A 39 LYS cc_start: 0.8144 (mttt) cc_final: 0.7563 (mtmt) REVERT: A 112 ASN cc_start: 0.7443 (t0) cc_final: 0.7182 (t0) REVERT: A 123 GLN cc_start: 0.7410 (OUTLIER) cc_final: 0.5430 (mp10) REVERT: A 126 ASP cc_start: 0.6984 (m-30) cc_final: 0.6412 (p0) REVERT: A 134 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7033 (tt0) REVERT: A 155 ASP cc_start: 0.8007 (t70) cc_final: 0.6962 (t0) REVERT: A 186 ASN cc_start: 0.7244 (m-40) cc_final: 0.6991 (m110) REVERT: A 198 ASN cc_start: 0.8066 (t0) cc_final: 0.7797 (p0) REVERT: A 229 GLU cc_start: 0.8273 (tt0) cc_final: 0.7993 (tt0) REVERT: A 243 ASP cc_start: 0.5762 (m-30) cc_final: 0.5494 (m-30) REVERT: A 267 ASP cc_start: 0.6238 (p0) cc_final: 0.5948 (p0) REVERT: A 289 ASP cc_start: 0.7590 (t70) cc_final: 0.7310 (t0) REVERT: A 328 MET cc_start: 0.6334 (mtp) cc_final: 0.5881 (mmt) REVERT: A 355 ARG cc_start: 0.6777 (mmt90) cc_final: 0.5844 (mtp180) REVERT: A 380 ARG cc_start: 0.7128 (ttp-170) cc_final: 0.6633 (mtp85) REVERT: A 428 LYS cc_start: 0.8288 (tttt) cc_final: 0.7883 (mtpp) REVERT: B 11 MET cc_start: 0.7864 (mmm) cc_final: 0.7510 (tpp) REVERT: B 15 GLN cc_start: 0.6904 (mm-40) cc_final: 0.6375 (mt0) REVERT: B 39 LYS cc_start: 0.8241 (mttt) cc_final: 0.7656 (mtmt) REVERT: B 123 GLN cc_start: 0.7346 (OUTLIER) cc_final: 0.5432 (mp10) REVERT: B 126 ASP cc_start: 0.7001 (m-30) cc_final: 0.6414 (p0) REVERT: B 134 GLU cc_start: 0.7648 (mt-10) cc_final: 0.6912 (tt0) REVERT: B 155 ASP cc_start: 0.8008 (t70) cc_final: 0.6889 (t0) REVERT: B 186 ASN cc_start: 0.7232 (m-40) cc_final: 0.6998 (m110) REVERT: B 198 ASN cc_start: 0.8030 (t0) cc_final: 0.7754 (p0) REVERT: B 229 GLU cc_start: 0.8245 (tt0) cc_final: 0.7974 (tt0) REVERT: B 243 ASP cc_start: 0.5684 (m-30) cc_final: 0.5434 (m-30) REVERT: B 267 ASP cc_start: 0.6234 (p0) cc_final: 0.5945 (p0) REVERT: B 355 ARG cc_start: 0.6781 (mmt90) cc_final: 0.5837 (tpt90) REVERT: B 380 ARG cc_start: 0.7116 (ttp-170) cc_final: 0.6625 (mtp85) REVERT: B 428 LYS cc_start: 0.8257 (tttt) cc_final: 0.7896 (mtpp) REVERT: D 11 MET cc_start: 0.7816 (mmm) cc_final: 0.7601 (tpp) REVERT: D 39 LYS cc_start: 0.8130 (mttt) cc_final: 0.7554 (mtmt) REVERT: D 112 ASN cc_start: 0.7445 (t0) cc_final: 0.7184 (t0) REVERT: D 123 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.5486 (mp10) REVERT: D 126 ASP cc_start: 0.6987 (m-30) cc_final: 0.6416 (p0) REVERT: D 134 GLU cc_start: 0.7593 (mt-10) cc_final: 0.7027 (tt0) REVERT: D 155 ASP cc_start: 0.7985 (t70) cc_final: 0.6961 (t0) REVERT: D 186 ASN cc_start: 0.7239 (m-40) cc_final: 0.6999 (m110) REVERT: D 229 GLU cc_start: 0.8245 (tt0) cc_final: 0.7985 (tt0) REVERT: D 267 ASP cc_start: 0.6288 (p0) cc_final: 0.5998 (p0) REVERT: D 328 MET cc_start: 0.6279 (mtp) cc_final: 0.5948 (mmt) REVERT: D 355 ARG cc_start: 0.6798 (mmt90) cc_final: 0.5796 (tpt90) REVERT: D 380 ARG cc_start: 0.7136 (ttp-170) cc_final: 0.6643 (mtp85) REVERT: D 428 LYS cc_start: 0.8258 (tttt) cc_final: 0.7845 (mtpp) REVERT: C 11 MET cc_start: 0.7875 (mmm) cc_final: 0.7514 (mmm) REVERT: C 39 LYS cc_start: 0.8251 (mttt) cc_final: 0.7661 (mtmt) REVERT: C 123 GLN cc_start: 0.7332 (OUTLIER) cc_final: 0.5416 (mp10) REVERT: C 126 ASP cc_start: 0.6977 (m-30) cc_final: 0.6402 (p0) REVERT: C 134 GLU cc_start: 0.7652 (mt-10) cc_final: 0.6906 (tt0) REVERT: C 155 ASP cc_start: 0.8048 (t70) cc_final: 0.6965 (t0) REVERT: C 229 GLU cc_start: 0.8257 (tt0) cc_final: 0.7983 (tt0) REVERT: C 243 ASP cc_start: 0.5880 (m-30) cc_final: 0.5587 (m-30) REVERT: C 267 ASP cc_start: 0.6202 (p0) cc_final: 0.5911 (p0) REVERT: C 275 ARG cc_start: 0.7664 (OUTLIER) cc_final: 0.7440 (mmt-90) REVERT: C 289 ASP cc_start: 0.7590 (t70) cc_final: 0.7318 (t0) REVERT: C 355 ARG cc_start: 0.6795 (mmt90) cc_final: 0.5847 (mtp180) REVERT: C 380 ARG cc_start: 0.7125 (ttp-170) cc_final: 0.6635 (mtp85) REVERT: C 428 LYS cc_start: 0.8243 (tttt) cc_final: 0.7898 (mtpp) outliers start: 10 outliers final: 9 residues processed: 216 average time/residue: 2.8593 time to fit residues: 675.0168 Evaluate side-chains 214 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 200 time to evaluate : 2.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 321 ASP Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 275 ARG Chi-restraints excluded: chain C residue 321 ASP Chi-restraints excluded: chain C residue 418 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 85 optimal weight: 0.8980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6390 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13840 Z= 0.217 Angle : 0.534 5.709 18776 Z= 0.264 Chirality : 0.045 0.137 2052 Planarity : 0.004 0.034 2448 Dihedral : 6.964 59.351 1956 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.25 % Allowed : 19.74 % Favored : 79.02 % 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: -1.39 (0.20), residues: 1708 helix: -1.21 (0.27), residues: 392 sheet: -0.86 (0.33), residues: 248 loop : -0.78 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 284 HIS 0.005 0.001 HIS D 257 PHE 0.016 0.001 PHE C 178 TYR 0.007 0.001 TYR C 309 ARG 0.003 0.000 ARG C 162 *********************** 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 215 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 201 time to evaluate : 2.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 LYS cc_start: 0.8139 (mttt) cc_final: 0.7559 (mtmt) REVERT: A 126 ASP cc_start: 0.6990 (m-30) cc_final: 0.6483 (p0) REVERT: A 134 GLU cc_start: 0.7601 (mt-10) cc_final: 0.7056 (tt0) REVERT: A 155 ASP cc_start: 0.8011 (t70) cc_final: 0.6924 (t0) REVERT: A 186 ASN cc_start: 0.7252 (m-40) cc_final: 0.6999 (m110) REVERT: A 198 ASN cc_start: 0.8058 (t0) cc_final: 0.7781 (p0) REVERT: A 229 GLU cc_start: 0.8284 (tt0) cc_final: 0.8033 (tt0) REVERT: A 243 ASP cc_start: 0.5602 (m-30) cc_final: 0.5384 (m-30) REVERT: A 267 ASP cc_start: 0.6149 (p0) cc_final: 0.5852 (p0) REVERT: A 328 MET cc_start: 0.6403 (mtp) cc_final: 0.5788 (mmt) REVERT: A 355 ARG cc_start: 0.6744 (mmt90) cc_final: 0.5806 (mtp180) REVERT: A 380 ARG cc_start: 0.7128 (ttp-170) cc_final: 0.6620 (mtp85) REVERT: A 428 LYS cc_start: 0.8288 (tttt) cc_final: 0.7882 (mtpp) REVERT: B 11 MET cc_start: 0.7824 (mmm) cc_final: 0.7622 (tpp) REVERT: B 39 LYS cc_start: 0.8131 (mttt) cc_final: 0.7560 (mtmt) REVERT: B 126 ASP cc_start: 0.7007 (m-30) cc_final: 0.6489 (p0) REVERT: B 134 GLU cc_start: 0.7697 (mt-10) cc_final: 0.6970 (tt0) REVERT: B 155 ASP cc_start: 0.8152 (t70) cc_final: 0.6981 (t0) REVERT: B 186 ASN cc_start: 0.7237 (m-40) cc_final: 0.6986 (m110) REVERT: B 198 ASN cc_start: 0.8022 (t0) cc_final: 0.7739 (p0) REVERT: B 213 MET cc_start: 0.8714 (mtm) cc_final: 0.8422 (mtp) REVERT: B 229 GLU cc_start: 0.8260 (tt0) cc_final: 0.7990 (tt0) REVERT: B 243 ASP cc_start: 0.5617 (m-30) cc_final: 0.5397 (m-30) REVERT: B 267 ASP cc_start: 0.6153 (p0) cc_final: 0.5860 (p0) REVERT: B 355 ARG cc_start: 0.6735 (mmt90) cc_final: 0.5806 (mtp180) REVERT: B 380 ARG cc_start: 0.7116 (ttp-170) cc_final: 0.6613 (mtp85) REVERT: B 428 LYS cc_start: 0.8240 (tttt) cc_final: 0.7891 (mtpp) REVERT: D 39 LYS cc_start: 0.8134 (mttt) cc_final: 0.7561 (mtmt) REVERT: D 112 ASN cc_start: 0.7446 (t0) cc_final: 0.7229 (t0) REVERT: D 126 ASP cc_start: 0.6995 (m-30) cc_final: 0.6489 (p0) REVERT: D 134 GLU cc_start: 0.7582 (mt-10) cc_final: 0.7066 (tt0) REVERT: D 155 ASP cc_start: 0.7971 (t70) cc_final: 0.6922 (t0) REVERT: D 186 ASN cc_start: 0.7231 (m-40) cc_final: 0.6979 (m110) REVERT: D 229 GLU cc_start: 0.8339 (tt0) cc_final: 0.8041 (tt0) REVERT: D 267 ASP cc_start: 0.6191 (p0) cc_final: 0.5896 (p0) REVERT: D 328 MET cc_start: 0.6334 (mtp) cc_final: 0.5833 (mmt) REVERT: D 355 ARG cc_start: 0.6743 (mmt90) cc_final: 0.5817 (mtp180) REVERT: D 380 ARG cc_start: 0.7138 (ttp-170) cc_final: 0.6634 (mtp85) REVERT: D 428 LYS cc_start: 0.8241 (tttt) cc_final: 0.7849 (mtpp) REVERT: C 39 LYS cc_start: 0.8135 (mttt) cc_final: 0.7556 (mtmt) REVERT: C 126 ASP cc_start: 0.6987 (m-30) cc_final: 0.6408 (p0) REVERT: C 134 GLU cc_start: 0.7675 (mt-10) cc_final: 0.6940 (tt0) REVERT: C 155 ASP cc_start: 0.7999 (t70) cc_final: 0.6889 (t0) REVERT: C 186 ASN cc_start: 0.7255 (m-40) cc_final: 0.6993 (m110) REVERT: C 229 GLU cc_start: 0.8270 (tt0) cc_final: 0.7998 (tt0) REVERT: C 243 ASP cc_start: 0.5606 (m-30) cc_final: 0.5388 (m-30) REVERT: C 267 ASP cc_start: 0.6119 (p0) cc_final: 0.5830 (p0) REVERT: C 275 ARG cc_start: 0.7587 (OUTLIER) cc_final: 0.7349 (mmt-90) REVERT: C 355 ARG cc_start: 0.6769 (mmt90) cc_final: 0.5815 (mtp180) REVERT: C 380 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6626 (mtp85) REVERT: C 428 LYS cc_start: 0.8244 (tttt) cc_final: 0.7892 (mtpp) outliers start: 14 outliers final: 8 residues processed: 213 average time/residue: 3.0533 time to fit residues: 707.0267 Evaluate side-chains 202 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 2.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain C residue 123 GLN Chi-restraints excluded: chain C residue 275 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 161 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13840 Z= 0.305 Angle : 0.546 5.884 18776 Z= 0.272 Chirality : 0.046 0.139 2052 Planarity : 0.004 0.034 2448 Dihedral : 6.991 60.902 1956 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.25 % Allowed : 19.88 % Favored : 78.88 % 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: -1.37 (0.20), residues: 1708 helix: -1.23 (0.26), residues: 396 sheet: -0.81 (0.33), residues: 248 loop : -0.76 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 284 HIS 0.004 0.001 HIS D 257 PHE 0.010 0.001 PHE B 178 TYR 0.010 0.001 TYR B 309 ARG 0.003 0.000 ARG B 162 *********************** 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 207 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 193 time to evaluate : 2.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.6822 (mm-40) cc_final: 0.6322 (mt0) REVERT: A 39 LYS cc_start: 0.8149 (mttt) cc_final: 0.7554 (mtmt) REVERT: A 126 ASP cc_start: 0.7004 (m-30) cc_final: 0.6495 (p0) REVERT: A 134 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7156 (tt0) REVERT: A 155 ASP cc_start: 0.7967 (t70) cc_final: 0.6886 (t0) REVERT: A 186 ASN cc_start: 0.7269 (m-40) cc_final: 0.6993 (m110) REVERT: A 198 ASN cc_start: 0.8054 (t0) cc_final: 0.7774 (p0) REVERT: A 229 GLU cc_start: 0.8344 (tt0) cc_final: 0.8076 (tt0) REVERT: A 243 ASP cc_start: 0.5664 (m-30) cc_final: 0.5433 (m-30) REVERT: A 267 ASP cc_start: 0.6137 (p0) cc_final: 0.5850 (p0) REVERT: A 328 MET cc_start: 0.6553 (mtp) cc_final: 0.5819 (mmt) REVERT: A 355 ARG cc_start: 0.6774 (mmt90) cc_final: 0.5738 (mtp180) REVERT: A 380 ARG cc_start: 0.7125 (ttp-170) cc_final: 0.6604 (mtp85) REVERT: A 428 LYS cc_start: 0.8299 (tttt) cc_final: 0.7889 (mtpp) REVERT: B 11 MET cc_start: 0.7831 (mmm) cc_final: 0.7554 (tpp) REVERT: B 15 GLN cc_start: 0.6845 (mm-40) cc_final: 0.6330 (mt0) REVERT: B 39 LYS cc_start: 0.8158 (mttt) cc_final: 0.7573 (mtmt) REVERT: B 126 ASP cc_start: 0.7021 (m-30) cc_final: 0.6506 (p0) REVERT: B 134 GLU cc_start: 0.7643 (mt-10) cc_final: 0.6963 (tt0) REVERT: B 155 ASP cc_start: 0.8160 (t70) cc_final: 0.6977 (t0) REVERT: B 186 ASN cc_start: 0.7246 (m-40) cc_final: 0.6971 (m110) REVERT: B 198 ASN cc_start: 0.8017 (t0) cc_final: 0.7732 (p0) REVERT: B 229 GLU cc_start: 0.8337 (tt0) cc_final: 0.8079 (tt0) REVERT: B 243 ASP cc_start: 0.5668 (m-30) cc_final: 0.5434 (m-30) REVERT: B 267 ASP cc_start: 0.6161 (p0) cc_final: 0.5867 (p0) REVERT: B 355 ARG cc_start: 0.6744 (mmt90) cc_final: 0.5724 (mtp180) REVERT: B 380 ARG cc_start: 0.7098 (ttp-170) cc_final: 0.6595 (mtp85) REVERT: B 428 LYS cc_start: 0.8262 (tttt) cc_final: 0.7906 (mtpp) REVERT: D 15 GLN cc_start: 0.6815 (mm-40) cc_final: 0.6340 (mt0) REVERT: D 39 LYS cc_start: 0.8141 (mttt) cc_final: 0.7550 (mtmt) REVERT: D 123 GLN cc_start: 0.7254 (OUTLIER) cc_final: 0.5422 (mp10) REVERT: D 126 ASP cc_start: 0.7006 (m-30) cc_final: 0.6501 (p0) REVERT: D 134 GLU cc_start: 0.7616 (mt-10) cc_final: 0.7158 (tt0) REVERT: D 155 ASP cc_start: 0.7994 (t70) cc_final: 0.6960 (t0) REVERT: D 186 ASN cc_start: 0.7257 (m-40) cc_final: 0.6999 (m110) REVERT: D 229 GLU cc_start: 0.8351 (tt0) cc_final: 0.8085 (tt0) REVERT: D 267 ASP cc_start: 0.6185 (p0) cc_final: 0.5891 (p0) REVERT: D 355 ARG cc_start: 0.6747 (mmt90) cc_final: 0.5733 (mtp180) REVERT: D 380 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6639 (mtp85) REVERT: D 428 LYS cc_start: 0.8263 (tttt) cc_final: 0.7863 (mtpp) REVERT: C 15 GLN cc_start: 0.6868 (mm-40) cc_final: 0.6373 (mt0) REVERT: C 39 LYS cc_start: 0.8144 (mttt) cc_final: 0.7549 (mtmt) REVERT: C 126 ASP cc_start: 0.6998 (m-30) cc_final: 0.6490 (p0) REVERT: C 134 GLU cc_start: 0.7635 (mt-10) cc_final: 0.6972 (tt0) REVERT: C 155 ASP cc_start: 0.8051 (t70) cc_final: 0.6951 (t0) REVERT: C 186 ASN cc_start: 0.7227 (m-40) cc_final: 0.6946 (m110) REVERT: C 229 GLU cc_start: 0.8348 (tt0) cc_final: 0.8089 (tt0) REVERT: C 243 ASP cc_start: 0.5629 (m-30) cc_final: 0.5402 (m-30) REVERT: C 267 ASP cc_start: 0.6111 (p0) cc_final: 0.5828 (p0) REVERT: C 355 ARG cc_start: 0.6747 (mmt90) cc_final: 0.5731 (mtp180) REVERT: C 380 ARG cc_start: 0.7132 (ttp-170) cc_final: 0.6620 (mtp85) REVERT: C 428 LYS cc_start: 0.8264 (tttt) cc_final: 0.7903 (mtpp) outliers start: 14 outliers final: 9 residues processed: 203 average time/residue: 3.0641 time to fit residues: 675.0495 Evaluate side-chains 196 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 186 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 MET Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 108 MET Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 418 THR Chi-restraints excluded: chain C residue 123 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 102 optimal weight: 4.9990 chunk 110 optimal weight: 0.9980 chunk 80 optimal weight: 3.9990 chunk 15 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 147 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.3030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 13840 Z= 0.322 Angle : 0.550 5.826 18776 Z= 0.274 Chirality : 0.046 0.139 2052 Planarity : 0.004 0.035 2448 Dihedral : 6.982 61.612 1956 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.90 % Allowed : 20.22 % Favored : 78.88 % 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: -1.35 (0.20), residues: 1708 helix: -1.22 (0.26), residues: 396 sheet: -0.78 (0.32), residues: 248 loop : -0.75 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 284 HIS 0.004 0.001 HIS A 257 PHE 0.016 0.001 PHE A 178 TYR 0.010 0.001 TYR D 309 ARG 0.002 0.000 ARG C 162 *********************** 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 201 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 2.237 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.6838 (mm-40) cc_final: 0.6311 (mt0) REVERT: A 39 LYS cc_start: 0.8188 (mttt) cc_final: 0.7596 (mtmt) REVERT: A 123 GLN cc_start: 0.7277 (OUTLIER) cc_final: 0.5541 (mp10) REVERT: A 126 ASP cc_start: 0.7027 (m-30) cc_final: 0.6521 (p0) REVERT: A 134 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7115 (tt0) REVERT: A 155 ASP cc_start: 0.7956 (t70) cc_final: 0.6873 (t0) REVERT: A 168 MET cc_start: 0.6849 (ttp) cc_final: 0.6640 (ttp) REVERT: A 186 ASN cc_start: 0.7268 (m-40) cc_final: 0.6993 (m110) REVERT: A 198 ASN cc_start: 0.8010 (t0) cc_final: 0.7708 (p0) REVERT: A 229 GLU cc_start: 0.8346 (tt0) cc_final: 0.8104 (tt0) REVERT: A 243 ASP cc_start: 0.5643 (m-30) cc_final: 0.5428 (m-30) REVERT: A 267 ASP cc_start: 0.6158 (p0) cc_final: 0.5863 (p0) REVERT: A 328 MET cc_start: 0.6695 (mtp) cc_final: 0.5834 (mmt) REVERT: A 355 ARG cc_start: 0.6728 (mmt90) cc_final: 0.5671 (mtp180) REVERT: A 380 ARG cc_start: 0.7072 (ttp-170) cc_final: 0.6558 (mtp85) REVERT: A 428 LYS cc_start: 0.8300 (tttt) cc_final: 0.7894 (mtpp) REVERT: B 11 MET cc_start: 0.7847 (mmm) cc_final: 0.7561 (tpp) REVERT: B 15 GLN cc_start: 0.6853 (mm-40) cc_final: 0.6313 (mt0) REVERT: B 39 LYS cc_start: 0.8152 (mttt) cc_final: 0.7550 (mtmt) REVERT: B 123 GLN cc_start: 0.7312 (OUTLIER) cc_final: 0.5558 (mp10) REVERT: B 126 ASP cc_start: 0.7006 (m-30) cc_final: 0.6514 (p0) REVERT: B 134 GLU cc_start: 0.7543 (mt-10) cc_final: 0.7035 (tt0) REVERT: B 155 ASP cc_start: 0.8166 (t70) cc_final: 0.6992 (t0) REVERT: B 186 ASN cc_start: 0.7253 (m-40) cc_final: 0.6968 (m110) REVERT: B 198 ASN cc_start: 0.8012 (t0) cc_final: 0.7721 (p0) REVERT: B 229 GLU cc_start: 0.8358 (tt0) cc_final: 0.8127 (tt0) REVERT: B 243 ASP cc_start: 0.5669 (m-30) cc_final: 0.5440 (m-30) REVERT: B 267 ASP cc_start: 0.6183 (p0) cc_final: 0.5882 (p0) REVERT: B 355 ARG cc_start: 0.6771 (mmt90) cc_final: 0.5722 (mtp180) REVERT: B 380 ARG cc_start: 0.7103 (ttp-170) cc_final: 0.6603 (mtp85) REVERT: B 428 LYS cc_start: 0.8270 (tttt) cc_final: 0.7913 (mtpp) REVERT: D 15 GLN cc_start: 0.6836 (mm-40) cc_final: 0.6332 (mt0) REVERT: D 39 LYS cc_start: 0.8181 (mttt) cc_final: 0.7593 (mtmt) REVERT: D 126 ASP cc_start: 0.7032 (m-30) cc_final: 0.6525 (p0) REVERT: D 134 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7138 (tt0) REVERT: D 155 ASP cc_start: 0.7985 (t70) cc_final: 0.6941 (t0) REVERT: D 186 ASN cc_start: 0.7272 (m-40) cc_final: 0.7025 (m110) REVERT: D 229 GLU cc_start: 0.8369 (tt0) cc_final: 0.8102 (tt0) REVERT: D 267 ASP cc_start: 0.6201 (p0) cc_final: 0.5898 (p0) REVERT: D 328 MET cc_start: 0.6149 (mtp) cc_final: 0.5912 (mmt) REVERT: D 355 ARG cc_start: 0.6770 (mmt90) cc_final: 0.5726 (mtp180) REVERT: D 380 ARG cc_start: 0.7120 (ttp-170) cc_final: 0.6616 (mtp85) REVERT: D 428 LYS cc_start: 0.8272 (tttt) cc_final: 0.7872 (mtpp) REVERT: C 15 GLN cc_start: 0.6889 (mm-40) cc_final: 0.6364 (mt0) REVERT: C 39 LYS cc_start: 0.8165 (mttt) cc_final: 0.7556 (mtmt) REVERT: C 123 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.5559 (mp10) REVERT: C 126 ASP cc_start: 0.7067 (m-30) cc_final: 0.6536 (p0) REVERT: C 134 GLU cc_start: 0.7534 (mt-10) cc_final: 0.7021 (tt0) REVERT: C 155 ASP cc_start: 0.8071 (t70) cc_final: 0.6963 (t0) REVERT: C 186 ASN cc_start: 0.7229 (m-40) cc_final: 0.6951 (m110) REVERT: C 229 GLU cc_start: 0.8364 (tt0) cc_final: 0.8105 (tt0) REVERT: C 243 ASP cc_start: 0.5645 (m-30) cc_final: 0.5429 (m-30) REVERT: C 267 ASP cc_start: 0.6142 (p0) cc_final: 0.5844 (p0) REVERT: C 355 ARG cc_start: 0.6778 (mmt90) cc_final: 0.5729 (mtp180) REVERT: C 380 ARG cc_start: 0.7131 (ttp-170) cc_final: 0.6623 (mtp85) REVERT: C 428 LYS cc_start: 0.8276 (tttt) cc_final: 0.7913 (mtpp) outliers start: 9 outliers final: 5 residues processed: 199 average time/residue: 2.9752 time to fit residues: 645.1763 Evaluate side-chains 194 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 186 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 123 GLN Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain B residue 289 ASP Chi-restraints excluded: chain D residue 123 GLN Chi-restraints excluded: chain D residue 289 ASP Chi-restraints excluded: chain D residue 321 ASP Chi-restraints excluded: chain C residue 123 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.7980 chunk 141 optimal weight: 0.0870 chunk 150 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 118 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 142 optimal weight: 0.6980 chunk 99 optimal weight: 4.9990 chunk 159 optimal weight: 3.9990 overall best weight: 0.9162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6374 moved from start: 0.3105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13840 Z= 0.155 Angle : 0.515 5.752 18776 Z= 0.254 Chirality : 0.045 0.136 2052 Planarity : 0.004 0.034 2448 Dihedral : 6.682 57.592 1956 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.83 % Allowed : 20.08 % Favored : 79.09 % 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: -1.07 (0.20), residues: 1708 helix: -0.90 (0.27), residues: 396 sheet: -0.72 (0.32), residues: 248 loop : -0.57 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 274 HIS 0.004 0.001 HIS A 257 PHE 0.016 0.001 PHE C 178 TYR 0.007 0.001 TYR C 309 ARG 0.002 0.000 ARG B 162 *********************** 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 196 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLN cc_start: 0.6800 (mm-40) cc_final: 0.6269 (mt0) REVERT: A 39 LYS cc_start: 0.8183 (mttt) cc_final: 0.7599 (mtmt) REVERT: A 126 ASP cc_start: 0.7027 (m-30) cc_final: 0.6524 (p0) REVERT: A 134 GLU cc_start: 0.7546 (mt-10) cc_final: 0.7091 (tt0) REVERT: A 155 ASP cc_start: 0.7947 (t70) cc_final: 0.6839 (t0) REVERT: A 168 MET cc_start: 0.6885 (ttp) cc_final: 0.6631 (ttp) REVERT: A 186 ASN cc_start: 0.7212 (m-40) cc_final: 0.6940 (m110) REVERT: A 198 ASN cc_start: 0.8003 (t0) cc_final: 0.7698 (p0) REVERT: A 229 GLU cc_start: 0.8308 (tt0) cc_final: 0.8059 (tt0) REVERT: A 243 ASP cc_start: 0.5533 (m-30) cc_final: 0.5324 (m-30) REVERT: A 267 ASP cc_start: 0.6037 (p0) cc_final: 0.5747 (p0) REVERT: A 328 MET cc_start: 0.6592 (mtp) cc_final: 0.5688 (mmt) REVERT: A 355 ARG cc_start: 0.6668 (mmt90) cc_final: 0.5654 (mtp180) REVERT: A 380 ARG cc_start: 0.7056 (ttp-170) cc_final: 0.6541 (mtp85) REVERT: A 428 LYS cc_start: 0.8278 (tttt) cc_final: 0.7888 (mtpp) REVERT: B 11 MET cc_start: 0.7775 (mmm) cc_final: 0.7555 (tpp) REVERT: B 15 GLN cc_start: 0.6800 (mm-40) cc_final: 0.6265 (mt0) REVERT: B 39 LYS cc_start: 0.8151 (mttt) cc_final: 0.7560 (mtmt) REVERT: B 126 ASP cc_start: 0.7010 (m-30) cc_final: 0.6520 (p0) REVERT: B 134 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7064 (tt0) REVERT: B 155 ASP cc_start: 0.8114 (t70) cc_final: 0.6905 (t0) REVERT: B 186 ASN cc_start: 0.7175 (m-40) cc_final: 0.6892 (m110) REVERT: B 198 ASN cc_start: 0.8004 (t0) cc_final: 0.7710 (p0) REVERT: B 229 GLU cc_start: 0.8282 (tt0) cc_final: 0.8047 (tt0) REVERT: B 243 ASP cc_start: 0.5595 (m-30) cc_final: 0.5385 (m-30) REVERT: B 267 ASP cc_start: 0.6042 (p0) cc_final: 0.5749 (p0) REVERT: B 355 ARG cc_start: 0.6672 (mmt90) cc_final: 0.5648 (mtp180) REVERT: B 380 ARG cc_start: 0.7100 (ttp-170) cc_final: 0.6576 (mtp85) REVERT: B 428 LYS cc_start: 0.8246 (tttt) cc_final: 0.7902 (mtpp) REVERT: D 15 GLN cc_start: 0.6788 (mm-40) cc_final: 0.6288 (mt0) REVERT: D 39 LYS cc_start: 0.8155 (mttt) cc_final: 0.7571 (mtmt) REVERT: D 126 ASP cc_start: 0.7033 (m-30) cc_final: 0.6531 (p0) REVERT: D 134 GLU cc_start: 0.7563 (mt-10) cc_final: 0.7137 (tt0) REVERT: D 155 ASP cc_start: 0.7920 (t70) cc_final: 0.6861 (t0) REVERT: D 186 ASN cc_start: 0.7231 (m-40) cc_final: 0.6965 (m110) REVERT: D 229 GLU cc_start: 0.8385 (tt0) cc_final: 0.8141 (tt0) REVERT: D 267 ASP cc_start: 0.6078 (p0) cc_final: 0.5785 (p0) REVERT: D 355 ARG cc_start: 0.6675 (mmt90) cc_final: 0.5655 (mtp180) REVERT: D 380 ARG cc_start: 0.7119 (ttp-170) cc_final: 0.6611 (mtp85) REVERT: D 428 LYS cc_start: 0.8248 (tttt) cc_final: 0.7866 (mtpp) REVERT: C 15 GLN cc_start: 0.6859 (mm-40) cc_final: 0.6344 (mt0) REVERT: C 39 LYS cc_start: 0.8150 (mttt) cc_final: 0.7561 (mtmt) REVERT: C 126 ASP cc_start: 0.7069 (m-30) cc_final: 0.6543 (p0) REVERT: C 134 GLU cc_start: 0.7624 (mt-10) cc_final: 0.7060 (tt0) REVERT: C 155 ASP cc_start: 0.7939 (t70) cc_final: 0.6811 (t0) REVERT: C 186 ASN cc_start: 0.7192 (m-40) cc_final: 0.6917 (m110) REVERT: C 229 GLU cc_start: 0.8291 (tt0) cc_final: 0.8057 (tt0) REVERT: C 243 ASP cc_start: 0.5606 (m-30) cc_final: 0.5391 (m-30) REVERT: C 267 ASP cc_start: 0.6015 (p0) cc_final: 0.5725 (p0) REVERT: C 355 ARG cc_start: 0.6678 (mmt90) cc_final: 0.5654 (mtp180) REVERT: C 380 ARG cc_start: 0.7130 (ttp-170) cc_final: 0.6600 (mtp85) REVERT: C 428 LYS cc_start: 0.8250 (tttt) cc_final: 0.7868 (mtpp) outliers start: 8 outliers final: 3 residues processed: 193 average time/residue: 3.0440 time to fit residues: 642.6951 Evaluate side-chains 185 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 182 time to evaluate : 2.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain B residue 123 GLN Chi-restraints excluded: chain C residue 123 GLN 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: 2.9990 chunk 110 optimal weight: 0.5980 chunk 167 optimal weight: 0.8980 chunk 154 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 102 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 141 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 13840 Z= 0.157 Angle : 0.511 5.707 18776 Z= 0.251 Chirality : 0.044 0.136 2052 Planarity : 0.004 0.035 2448 Dihedral : 6.240 55.839 1950 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.55 % Allowed : 20.15 % Favored : 79.29 % 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: -0.91 (0.20), residues: 1708 helix: -0.66 (0.27), residues: 396 sheet: -0.66 (0.32), residues: 248 loop : -0.50 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 284 HIS 0.003 0.000 HIS D 257 PHE 0.011 0.001 PHE A 178 TYR 0.006 0.001 TYR B 309 ARG 0.002 0.000 ARG B 162 ********************** 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 192 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 188 time to evaluate : 2.430 Fit side-chains revert: symmetry clash REVERT: A 15 GLN cc_start: 0.6797 (mm-40) cc_final: 0.6261 (mt0) REVERT: A 39 LYS cc_start: 0.8186 (mttt) cc_final: 0.7609 (mtmt) REVERT: A 126 ASP cc_start: 0.7019 (m-30) cc_final: 0.6521 (p0) REVERT: A 134 GLU cc_start: 0.7623 (mt-10) cc_final: 0.7162 (tt0) REVERT: A 155 ASP cc_start: 0.7944 (t70) cc_final: 0.6819 (t0) REVERT: A 168 MET cc_start: 0.6870 (ttp) cc_final: 0.6574 (ttp) REVERT: A 186 ASN cc_start: 0.7184 (m-40) cc_final: 0.6901 (m110) REVERT: A 198 ASN cc_start: 0.8001 (t0) cc_final: 0.7693 (p0) REVERT: A 229 GLU cc_start: 0.8285 (tt0) cc_final: 0.8065 (tt0) REVERT: A 267 ASP cc_start: 0.5944 (p0) cc_final: 0.5663 (p0) REVERT: A 328 MET cc_start: 0.6528 (mtp) cc_final: 0.5850 (mmt) REVERT: A 355 ARG cc_start: 0.6658 (mmt90) cc_final: 0.5632 (mtp180) REVERT: A 380 ARG cc_start: 0.7096 (ttp-170) cc_final: 0.6572 (mtp85) REVERT: A 428 LYS cc_start: 0.8284 (tttt) cc_final: 0.7889 (mtpp) REVERT: B 11 MET cc_start: 0.7793 (mmm) cc_final: 0.7553 (tpp) REVERT: B 15 GLN cc_start: 0.6798 (mm-40) cc_final: 0.6230 (mt0) REVERT: B 39 LYS cc_start: 0.8189 (mttt) cc_final: 0.7621 (mtmt) REVERT: B 126 ASP cc_start: 0.7007 (m-30) cc_final: 0.6524 (p0) REVERT: B 134 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7060 (tt0) REVERT: B 155 ASP cc_start: 0.8140 (t70) cc_final: 0.6945 (t0) REVERT: B 198 ASN cc_start: 0.8003 (t0) cc_final: 0.7705 (p0) REVERT: B 229 GLU cc_start: 0.8290 (tt0) cc_final: 0.8076 (tt0) REVERT: B 267 ASP cc_start: 0.5950 (p0) cc_final: 0.5666 (p0) REVERT: B 355 ARG cc_start: 0.6655 (mmt90) cc_final: 0.5625 (mtp180) REVERT: B 380 ARG cc_start: 0.7103 (ttp-170) cc_final: 0.6586 (mtp85) REVERT: B 428 LYS cc_start: 0.8245 (tttt) cc_final: 0.7900 (mtpp) REVERT: D 15 GLN cc_start: 0.6780 (mm-40) cc_final: 0.6287 (mt0) REVERT: D 39 LYS cc_start: 0.8188 (mttt) cc_final: 0.7620 (mtmt) REVERT: D 126 ASP cc_start: 0.7028 (m-30) cc_final: 0.6531 (p0) REVERT: D 134 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7191 (tt0) REVERT: D 155 ASP cc_start: 0.7925 (t70) cc_final: 0.6814 (t0) REVERT: D 186 ASN cc_start: 0.7226 (m-40) cc_final: 0.6964 (m110) REVERT: D 229 GLU cc_start: 0.8320 (tt0) cc_final: 0.8077 (tt0) REVERT: D 267 ASP cc_start: 0.5978 (p0) cc_final: 0.5696 (p0) REVERT: D 355 ARG cc_start: 0.6659 (mmt90) cc_final: 0.5632 (mtp180) REVERT: D 380 ARG cc_start: 0.7120 (ttp-170) cc_final: 0.6604 (mtp85) REVERT: D 428 LYS cc_start: 0.8249 (tttt) cc_final: 0.7862 (mtpp) REVERT: C 15 GLN cc_start: 0.6835 (mm-40) cc_final: 0.6311 (mt0) REVERT: C 39 LYS cc_start: 0.8181 (mttt) cc_final: 0.7606 (mtmt) REVERT: C 126 ASP cc_start: 0.7067 (m-30) cc_final: 0.6548 (p0) REVERT: C 134 GLU cc_start: 0.7558 (mt-10) cc_final: 0.7004 (tt0) REVERT: C 155 ASP cc_start: 0.8087 (t70) cc_final: 0.6928 (t0) REVERT: C 186 ASN cc_start: 0.7196 (m-40) cc_final: 0.6915 (m110) REVERT: C 229 GLU cc_start: 0.8311 (tt0) cc_final: 0.8076 (tt0) REVERT: C 243 ASP cc_start: 0.5602 (m-30) cc_final: 0.5396 (m-30) REVERT: C 267 ASP cc_start: 0.5921 (p0) cc_final: 0.5641 (p0) REVERT: C 355 ARG cc_start: 0.6659 (mmt90) cc_final: 0.5629 (mtp180) REVERT: C 380 ARG cc_start: 0.7124 (ttp-170) cc_final: 0.6609 (mtp85) REVERT: C 428 LYS cc_start: 0.8256 (tttt) cc_final: 0.7906 (mtpp) outliers start: 4 outliers final: 1 residues processed: 191 average time/residue: 3.0165 time to fit residues: 627.8289 Evaluate side-chains 185 residues out of total 1460 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 184 time to evaluate : 2.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 19 optimal weight: 0.0370 chunk 37 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 117 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 overall best weight: 1.0860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.103417 restraints weight = 82074.233| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.23 r_work: 0.3008 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 13840 Z= 0.169 Angle : 0.510 5.698 18776 Z= 0.250 Chirality : 0.045 0.137 2052 Planarity : 0.004 0.042 2448 Dihedral : 5.855 55.322 1944 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.42 % Allowed : 20.36 % Favored : 79.22 % 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: -0.80 (0.20), residues: 1708 helix: -0.52 (0.28), residues: 396 sheet: -0.57 (0.32), residues: 248 loop : -0.45 (0.19), residues: 1064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 284 HIS 0.003 0.000 HIS D 257 PHE 0.011 0.001 PHE D 178 TYR 0.007 0.001 TYR D 309 ARG 0.002 0.000 ARG C 162 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11261.78 seconds wall clock time: 197 minutes 56.18 seconds (11876.18 seconds total)