Starting phenix.real_space_refine on Sat Feb 17 04:56:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/02_2024/6lmt_0919.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/02_2024/6lmt_0919.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/02_2024/6lmt_0919.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/02_2024/6lmt_0919.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/02_2024/6lmt_0919.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lmt_0919/02_2024/6lmt_0919.pdb" } resolution = 2.66 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 11688 2.51 5 N 2696 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None 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: 17552 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "C" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "G" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 2054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 2054 Classifications: {'peptide': 254} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 244} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 175 Unusual residues: {'Y01': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "B" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "E" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 140 Unusual residues: {'Y01': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 9.46, per 1000 atoms: 0.54 Number of scatterers: 17552 At special positions: 0 Unit cell: (123.67, 123.67, 100.43, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 2976 8.00 N 2696 7.00 C 11688 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 41 " - pdb=" SG CYS A 126 " distance=2.04 Simple disulfide: pdb=" SG CYS A 43 " - pdb=" SG CYS A 160 " distance=2.01 Simple disulfide: pdb=" SG CYS B 41 " - pdb=" SG CYS B 126 " distance=2.04 Simple disulfide: pdb=" SG CYS B 43 " - pdb=" SG CYS B 160 " distance=2.01 Simple disulfide: pdb=" SG CYS C 41 " - pdb=" SG CYS C 126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 160 " distance=2.01 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 126 " distance=2.04 Simple disulfide: pdb=" SG CYS D 43 " - pdb=" SG CYS D 160 " distance=2.01 Simple disulfide: pdb=" SG CYS E 41 " - pdb=" SG CYS E 126 " distance=2.04 Simple disulfide: pdb=" SG CYS E 43 " - pdb=" SG CYS E 160 " distance=2.01 Simple disulfide: pdb=" SG CYS F 41 " - pdb=" SG CYS F 126 " distance=2.04 Simple disulfide: pdb=" SG CYS F 43 " - pdb=" SG CYS F 160 " distance=2.01 Simple disulfide: pdb=" SG CYS G 41 " - pdb=" SG CYS G 126 " distance=2.04 Simple disulfide: pdb=" SG CYS G 43 " - pdb=" SG CYS G 160 " distance=2.01 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 126 " distance=2.04 Simple disulfide: pdb=" SG CYS H 43 " - pdb=" SG CYS H 160 " distance=2.01 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: 6.39 Conformation dependent library (CDL) restraints added in 2.8 seconds 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3888 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 0 sheets defined 85.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 8 through 14 Processing helix chain 'A' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY A 24 " --> pdb=" O ASN A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Proline residue: A 59 - end of helix Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 91 through 106 Processing helix chain 'A' and resid 107 through 121 Processing helix chain 'A' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER A 129 " --> pdb=" O LEU A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 132 No H-bonds generated for 'chain 'A' and resid 130 through 132' Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 147 through 156 Processing helix chain 'A' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 203 Processing helix chain 'A' and resid 204 through 206 No H-bonds generated for 'chain 'A' and resid 204 through 206' Processing helix chain 'A' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE A 239 " --> pdb=" O HIS A 235 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN A 250 " --> pdb=" O GLN A 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY A 253 " --> pdb=" O GLU A 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 14 Processing helix chain 'B' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY B 24 " --> pdb=" O ASN B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU B 56 " --> pdb=" O GLY B 52 " (cutoff:3.500A) Proline residue: B 59 - end of helix Processing helix chain 'B' and resid 73 through 83 Processing helix chain 'B' and resid 91 through 106 Processing helix chain 'B' and resid 107 through 121 Processing helix chain 'B' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 132 No H-bonds generated for 'chain 'B' and resid 130 through 132' Processing helix chain 'B' and resid 133 through 137 Processing helix chain 'B' and resid 147 through 156 Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE B 164 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 203 Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE B 239 " --> pdb=" O HIS B 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN B 250 " --> pdb=" O GLN B 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY B 253 " --> pdb=" O GLU B 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN B 257 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 14 Processing helix chain 'C' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY C 24 " --> pdb=" O ASN C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 71 removed outlier: 3.681A pdb=" N LEU C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Proline residue: C 59 - end of helix Processing helix chain 'C' and resid 73 through 83 Processing helix chain 'C' and resid 91 through 106 Processing helix chain 'C' and resid 107 through 121 Processing helix chain 'C' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER C 129 " --> pdb=" O LEU C 125 " (cutoff:3.500A) Processing helix chain 'C' and resid 130 through 132 No H-bonds generated for 'chain 'C' and resid 130 through 132' Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 147 through 156 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE C 164 " --> pdb=" O LYS C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 203 Processing helix chain 'C' and resid 204 through 206 No H-bonds generated for 'chain 'C' and resid 204 through 206' Processing helix chain 'C' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE C 239 " --> pdb=" O HIS C 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN C 250 " --> pdb=" O GLN C 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY C 253 " --> pdb=" O GLU C 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN C 257 " --> pdb=" O GLY C 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 14 Processing helix chain 'D' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY D 24 " --> pdb=" O ASN D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU D 56 " --> pdb=" O GLY D 52 " (cutoff:3.500A) Proline residue: D 59 - end of helix Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 91 through 106 Processing helix chain 'D' and resid 107 through 121 Processing helix chain 'D' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER D 129 " --> pdb=" O LEU D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 132 No H-bonds generated for 'chain 'D' and resid 130 through 132' Processing helix chain 'D' and resid 133 through 137 Processing helix chain 'D' and resid 147 through 156 Processing helix chain 'D' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE D 164 " --> pdb=" O LYS D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 166 through 203 Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE D 239 " --> pdb=" O HIS D 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN D 250 " --> pdb=" O GLN D 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY D 253 " --> pdb=" O GLU D 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN D 257 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 14 Processing helix chain 'E' and resid 20 through 37 removed outlier: 3.947A pdb=" N GLY E 24 " --> pdb=" O ASN E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU E 56 " --> pdb=" O GLY E 52 " (cutoff:3.500A) Proline residue: E 59 - end of helix Processing helix chain 'E' and resid 73 through 83 Processing helix chain 'E' and resid 91 through 106 Processing helix chain 'E' and resid 107 through 121 Processing helix chain 'E' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER E 129 " --> pdb=" O LEU E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 130 through 132 No H-bonds generated for 'chain 'E' and resid 130 through 132' Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 147 through 156 Processing helix chain 'E' and resid 160 through 164 removed outlier: 3.622A pdb=" N PHE E 164 " --> pdb=" O LYS E 161 " (cutoff:3.500A) Processing helix chain 'E' and resid 166 through 203 Processing helix chain 'E' and resid 204 through 206 No H-bonds generated for 'chain 'E' and resid 204 through 206' Processing helix chain 'E' and resid 209 through 259 removed outlier: 3.759A pdb=" N PHE E 239 " --> pdb=" O HIS E 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN E 250 " --> pdb=" O GLN E 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY E 253 " --> pdb=" O GLU E 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN E 257 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing helix chain 'F' and resid 8 through 14 Processing helix chain 'F' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY F 24 " --> pdb=" O ASN F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU F 56 " --> pdb=" O GLY F 52 " (cutoff:3.500A) Proline residue: F 59 - end of helix Processing helix chain 'F' and resid 73 through 83 Processing helix chain 'F' and resid 91 through 106 Processing helix chain 'F' and resid 107 through 121 Processing helix chain 'F' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER F 129 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 132 No H-bonds generated for 'chain 'F' and resid 130 through 132' Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 147 through 156 Processing helix chain 'F' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE F 164 " --> pdb=" O LYS F 161 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 203 Processing helix chain 'F' and resid 204 through 206 No H-bonds generated for 'chain 'F' and resid 204 through 206' Processing helix chain 'F' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE F 239 " --> pdb=" O HIS F 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN F 250 " --> pdb=" O GLN F 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY F 253 " --> pdb=" O GLU F 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN F 257 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 14 Processing helix chain 'G' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY G 24 " --> pdb=" O ASN G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU G 56 " --> pdb=" O GLY G 52 " (cutoff:3.500A) Proline residue: G 59 - end of helix Processing helix chain 'G' and resid 73 through 83 Processing helix chain 'G' and resid 91 through 106 Processing helix chain 'G' and resid 107 through 121 Processing helix chain 'G' and resid 121 through 129 removed outlier: 3.559A pdb=" N SER G 129 " --> pdb=" O LEU G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 130 through 132 No H-bonds generated for 'chain 'G' and resid 130 through 132' Processing helix chain 'G' and resid 133 through 137 Processing helix chain 'G' and resid 147 through 156 Processing helix chain 'G' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE G 164 " --> pdb=" O LYS G 161 " (cutoff:3.500A) Processing helix chain 'G' and resid 166 through 203 Processing helix chain 'G' and resid 204 through 206 No H-bonds generated for 'chain 'G' and resid 204 through 206' Processing helix chain 'G' and resid 209 through 259 removed outlier: 3.761A pdb=" N PHE G 239 " --> pdb=" O HIS G 235 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASN G 250 " --> pdb=" O GLN G 246 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLY G 253 " --> pdb=" O GLU G 249 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ASN G 257 " --> pdb=" O GLY G 253 " (cutoff:3.500A) Processing helix chain 'H' and resid 8 through 14 Processing helix chain 'H' and resid 20 through 37 removed outlier: 3.946A pdb=" N GLY H 24 " --> pdb=" O ASN H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 47 through 71 removed outlier: 3.682A pdb=" N LEU H 56 " --> pdb=" O GLY H 52 " (cutoff:3.500A) Proline residue: H 59 - end of helix Processing helix chain 'H' and resid 73 through 83 Processing helix chain 'H' and resid 91 through 106 Processing helix chain 'H' and resid 107 through 121 Processing helix chain 'H' and resid 121 through 129 removed outlier: 3.560A pdb=" N SER H 129 " --> pdb=" O LEU H 125 " (cutoff:3.500A) Processing helix chain 'H' and resid 130 through 132 No H-bonds generated for 'chain 'H' and resid 130 through 132' Processing helix chain 'H' and resid 133 through 137 Processing helix chain 'H' and resid 147 through 156 Processing helix chain 'H' and resid 160 through 164 removed outlier: 3.623A pdb=" N PHE H 164 " --> pdb=" O LYS H 161 " (cutoff:3.500A) Processing helix chain 'H' and resid 166 through 203 Processing helix chain 'H' and resid 204 through 206 No H-bonds generated for 'chain 'H' and resid 204 through 206' Processing helix chain 'H' and resid 209 through 259 removed outlier: 3.760A pdb=" N PHE H 239 " --> pdb=" O HIS H 235 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N ASN H 250 " --> pdb=" O GLN H 246 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLY H 253 " --> pdb=" O GLU H 249 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ASN H 257 " --> pdb=" O GLY H 253 " (cutoff:3.500A) 1224 hydrogen bonds defined for protein. 3600 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: 4.61 Time building geometry restraints manager: 6.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2847 1.32 - 1.45: 4847 1.45 - 1.57: 10082 1.57 - 1.70: 0 1.70 - 1.82: 296 Bond restraints: 18072 Sorted by residual: bond pdb=" CB MET G 98 " pdb=" CG MET G 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CB MET A 98 " pdb=" CG MET A 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.48e+00 bond pdb=" CB MET E 98 " pdb=" CG MET E 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.43e+00 bond pdb=" CB MET C 98 " pdb=" CG MET C 98 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.43e+00 bond pdb=" CB MET B 98 " pdb=" CG MET B 98 " ideal model delta sigma weight residual 1.520 1.445 0.075 3.00e-02 1.11e+03 6.31e+00 ... (remaining 18067 not shown) Histogram of bond angle deviations from ideal: 96.57 - 104.06: 375 104.06 - 111.56: 7464 111.56 - 119.05: 7277 119.05 - 126.54: 9196 126.54 - 134.04: 256 Bond angle restraints: 24568 Sorted by residual: angle pdb=" C GLN F 208 " pdb=" N ALA F 209 " pdb=" CA ALA F 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN B 208 " pdb=" N ALA B 209 " pdb=" CA ALA B 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN H 208 " pdb=" N ALA H 209 " pdb=" CA ALA H 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN D 208 " pdb=" N ALA D 209 " pdb=" CA ALA D 209 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C GLN G 208 " pdb=" N ALA G 209 " pdb=" CA ALA G 209 " ideal model delta sigma weight residual 121.54 132.06 -10.52 1.91e+00 2.74e-01 3.03e+01 ... (remaining 24563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.32: 11544 16.32 - 32.64: 536 32.64 - 48.95: 208 48.95 - 65.27: 48 65.27 - 81.59: 8 Dihedral angle restraints: 12344 sinusoidal: 6360 harmonic: 5984 Sorted by residual: dihedral pdb=" CA ALA E 209 " pdb=" C ALA E 209 " pdb=" N ALA E 210 " pdb=" CA ALA E 210 " ideal model delta harmonic sigma weight residual 180.00 155.65 24.35 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CA ALA C 209 " pdb=" C ALA C 209 " pdb=" N ALA C 210 " pdb=" CA ALA C 210 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.36e+01 dihedral pdb=" CA ALA G 209 " pdb=" C ALA G 209 " pdb=" N ALA G 210 " pdb=" CA ALA G 210 " ideal model delta harmonic sigma weight residual 180.00 155.69 24.31 0 5.00e+00 4.00e-02 2.36e+01 ... (remaining 12341 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1758 0.056 - 0.112: 779 0.112 - 0.168: 167 0.168 - 0.224: 8 0.224 - 0.280: 16 Chirality restraints: 2728 Sorted by residual: chirality pdb=" CBE Y01 C 402 " pdb=" CAP Y01 C 402 " pdb=" CBB Y01 C 402 " pdb=" CBI Y01 C 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CBE Y01 E 402 " pdb=" CAP Y01 E 402 " pdb=" CBB Y01 E 402 " pdb=" CBI Y01 E 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CBE Y01 G 402 " pdb=" CAP Y01 G 402 " pdb=" CBB Y01 G 402 " pdb=" CBI Y01 G 402 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 1.94e+00 ... (remaining 2725 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 137 " 0.027 2.00e-02 2.50e+03 2.38e-02 9.95e+00 pdb=" CG PHE C 137 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE C 137 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 137 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE C 137 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 137 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE C 137 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 137 " -0.027 2.00e-02 2.50e+03 2.38e-02 9.92e+00 pdb=" CG PHE G 137 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE G 137 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE G 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE G 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 137 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE G 137 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 137 " -0.027 2.00e-02 2.50e+03 2.38e-02 9.92e+00 pdb=" CG PHE A 137 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 137 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE A 137 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE A 137 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 137 " -0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 137 " -0.005 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 6367 2.91 - 3.41: 16743 3.41 - 3.90: 29038 3.90 - 4.40: 34172 4.40 - 4.90: 56210 Nonbonded interactions: 142530 Sorted by model distance: nonbonded pdb=" O ASN F 72 " pdb=" NH2 ARG F 225 " model vdw 2.409 2.520 nonbonded pdb=" O ASN H 72 " pdb=" NH2 ARG H 225 " model vdw 2.409 2.520 nonbonded pdb=" O ASN D 72 " pdb=" NH2 ARG D 225 " model vdw 2.409 2.520 nonbonded pdb=" O ASN B 72 " pdb=" NH2 ARG B 225 " model vdw 2.409 2.520 nonbonded pdb=" O ASN E 72 " pdb=" NH2 ARG E 225 " model vdw 2.409 2.520 ... (remaining 142525 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 260 or resid 401 through 403)) selection = (chain 'B' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'C' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'D' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'E' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'F' and (resid 7 through 260 or resid 401 through 403)) selection = (chain 'G' and (resid 7 through 260 or resid 401 through 403)) selection = chain 'H' } 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=1.00 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: 3.320 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 10.970 Check model and map are aligned: 0.270 Set scattering table: 0.170 Process input model: 43.770 Find NCS groups from input model: 1.270 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 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 : 0.012 0.125 18072 Z= 0.777 Angle : 1.138 15.192 24568 Z= 0.577 Chirality : 0.063 0.280 2728 Planarity : 0.008 0.057 2904 Dihedral : 11.689 81.587 8408 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % 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: -4.48 (0.12), residues: 2016 helix: -2.86 (0.08), residues: 1464 sheet: None (None), residues: 0 loop : -2.61 (0.20), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.006 TRP A 62 HIS 0.012 0.003 HIS G 219 PHE 0.055 0.005 PHE C 137 TYR 0.038 0.006 TYR G 47 ARG 0.013 0.002 ARG C 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 413 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 413 time to evaluate : 1.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 80 GLU cc_start: 0.7367 (mm-30) cc_final: 0.6952 (tp30) REVERT: A 148 GLU cc_start: 0.6668 (tp30) cc_final: 0.6332 (tm-30) REVERT: A 157 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.6402 (mtp85) REVERT: A 168 GLU cc_start: 0.7457 (tm-30) cc_final: 0.7242 (tm-30) REVERT: A 234 GLU cc_start: 0.7501 (pt0) cc_final: 0.6971 (tp30) REVERT: B 80 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6982 (tp30) REVERT: B 96 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6769 (ttm110) REVERT: B 148 GLU cc_start: 0.6476 (tp30) cc_final: 0.6196 (tm-30) REVERT: B 157 ARG cc_start: 0.6819 (mtm-85) cc_final: 0.6468 (mtt180) REVERT: B 168 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7113 (tm-30) REVERT: B 216 TYR cc_start: 0.7787 (t80) cc_final: 0.7442 (t80) REVERT: B 234 GLU cc_start: 0.7410 (pt0) cc_final: 0.6855 (tp30) REVERT: C 80 GLU cc_start: 0.7326 (mm-30) cc_final: 0.6903 (tp30) REVERT: C 96 ARG cc_start: 0.7010 (mtm-85) cc_final: 0.6700 (ttm110) REVERT: C 148 GLU cc_start: 0.6598 (tp30) cc_final: 0.6275 (tm-30) REVERT: C 157 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.6350 (mtp85) REVERT: C 234 GLU cc_start: 0.7498 (pt0) cc_final: 0.6978 (tp30) REVERT: D 80 GLU cc_start: 0.7371 (mm-30) cc_final: 0.6981 (tp30) REVERT: D 96 ARG cc_start: 0.7123 (mtm-85) cc_final: 0.6769 (ttm110) REVERT: D 148 GLU cc_start: 0.6476 (tp30) cc_final: 0.6198 (tm-30) REVERT: D 157 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.6471 (mtt180) REVERT: D 168 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7114 (tm-30) REVERT: D 216 TYR cc_start: 0.7793 (t80) cc_final: 0.7505 (t80) REVERT: D 234 GLU cc_start: 0.7411 (pt0) cc_final: 0.6856 (tp30) REVERT: E 80 GLU cc_start: 0.7323 (mm-30) cc_final: 0.6893 (tp30) REVERT: E 148 GLU cc_start: 0.6567 (tp30) cc_final: 0.6265 (tm-30) REVERT: E 157 ARG cc_start: 0.6780 (mtm-85) cc_final: 0.6362 (mtp85) REVERT: E 168 GLU cc_start: 0.7497 (tm-30) cc_final: 0.7267 (tm-30) REVERT: E 234 GLU cc_start: 0.7489 (pt0) cc_final: 0.6983 (tp30) REVERT: F 80 GLU cc_start: 0.7374 (mm-30) cc_final: 0.6983 (tp30) REVERT: F 96 ARG cc_start: 0.7125 (mtm-85) cc_final: 0.6772 (ttm110) REVERT: F 148 GLU cc_start: 0.6476 (tp30) cc_final: 0.6199 (tm-30) REVERT: F 157 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.6472 (mtt180) REVERT: F 168 GLU cc_start: 0.7334 (tm-30) cc_final: 0.7111 (tm-30) REVERT: F 216 TYR cc_start: 0.7795 (t80) cc_final: 0.7505 (t80) REVERT: F 234 GLU cc_start: 0.7412 (pt0) cc_final: 0.6858 (tp30) REVERT: G 80 GLU cc_start: 0.7366 (mm-30) cc_final: 0.6951 (tp30) REVERT: G 148 GLU cc_start: 0.6669 (tp30) cc_final: 0.6333 (tm-30) REVERT: G 157 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.6400 (mtp85) REVERT: G 168 GLU cc_start: 0.7458 (tm-30) cc_final: 0.7242 (tm-30) REVERT: G 234 GLU cc_start: 0.7501 (pt0) cc_final: 0.6972 (tp30) REVERT: H 80 GLU cc_start: 0.7370 (mm-30) cc_final: 0.6980 (tp30) REVERT: H 96 ARG cc_start: 0.7124 (mtm-85) cc_final: 0.6770 (ttm110) REVERT: H 148 GLU cc_start: 0.6477 (tp30) cc_final: 0.6199 (tm-30) REVERT: H 157 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6473 (mtt180) REVERT: H 168 GLU cc_start: 0.7336 (tm-30) cc_final: 0.7115 (tm-30) REVERT: H 216 TYR cc_start: 0.7786 (t80) cc_final: 0.7502 (t80) REVERT: H 234 GLU cc_start: 0.7413 (pt0) cc_final: 0.6857 (tp30) REVERT: H 241 LYS cc_start: 0.6237 (ttpt) cc_final: 0.6032 (mtmt) outliers start: 0 outliers final: 2 residues processed: 413 average time/residue: 1.7843 time to fit residues: 797.4844 Evaluate side-chains 324 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 322 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain E residue 162 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 102 optimal weight: 0.6980 chunk 80 optimal weight: 0.0980 chunk 156 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 116 optimal weight: 0.5980 chunk 181 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 HIS B 73 ASN B 235 HIS C 235 HIS D 73 ASN D 235 HIS E 235 HIS F 73 ASN F 235 HIS G 235 HIS H 73 ASN H 235 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 18072 Z= 0.223 Angle : 0.714 14.170 24568 Z= 0.348 Chirality : 0.041 0.251 2728 Planarity : 0.006 0.047 2904 Dihedral : 9.827 57.031 4468 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.18 % Allowed : 8.59 % Favored : 89.23 % 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: -0.11 (0.17), residues: 2016 helix: 0.40 (0.12), residues: 1512 sheet: None (None), residues: 0 loop : -1.26 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 217 HIS 0.003 0.001 HIS A 219 PHE 0.015 0.002 PHE B 64 TYR 0.016 0.002 TYR B 216 ARG 0.001 0.000 ARG C 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 313 time to evaluate : 1.987 Fit side-chains REVERT: A 7 MET cc_start: 0.5022 (mtp) cc_final: 0.4746 (mtp) REVERT: A 157 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6303 (mtp85) REVERT: A 228 PHE cc_start: 0.6979 (t80) cc_final: 0.6405 (t80) REVERT: A 241 LYS cc_start: 0.6916 (tptp) cc_final: 0.6460 (mttp) REVERT: B 7 MET cc_start: 0.4692 (mtp) cc_final: 0.4388 (mtp) REVERT: B 96 ARG cc_start: 0.6764 (mtm-85) cc_final: 0.6328 (ttm110) REVERT: B 241 LYS cc_start: 0.6705 (tptp) cc_final: 0.6180 (mtmt) REVERT: C 157 ARG cc_start: 0.6752 (mtm-85) cc_final: 0.6267 (mtp85) REVERT: C 228 PHE cc_start: 0.6978 (t80) cc_final: 0.6402 (t80) REVERT: C 237 LYS cc_start: 0.6112 (OUTLIER) cc_final: 0.5645 (ttmt) REVERT: C 241 LYS cc_start: 0.6743 (tptp) cc_final: 0.6324 (mttp) REVERT: D 7 MET cc_start: 0.4691 (mtp) cc_final: 0.4384 (mtp) REVERT: D 96 ARG cc_start: 0.6763 (mtm-85) cc_final: 0.6326 (ttm110) REVERT: D 241 LYS cc_start: 0.6706 (tptp) cc_final: 0.6189 (mtmt) REVERT: E 7 MET cc_start: 0.4995 (mtp) cc_final: 0.4720 (mtp) REVERT: E 157 ARG cc_start: 0.6740 (mtm-85) cc_final: 0.6264 (mtp85) REVERT: E 228 PHE cc_start: 0.6987 (t80) cc_final: 0.6359 (t80) REVERT: E 237 LYS cc_start: 0.6120 (OUTLIER) cc_final: 0.5655 (ttmt) REVERT: E 241 LYS cc_start: 0.6733 (tptp) cc_final: 0.6325 (mttp) REVERT: F 96 ARG cc_start: 0.6765 (mtm-85) cc_final: 0.6328 (ttm110) REVERT: F 228 PHE cc_start: 0.6853 (t80) cc_final: 0.6529 (t80) REVERT: F 241 LYS cc_start: 0.6701 (tptp) cc_final: 0.6194 (mtmt) REVERT: G 7 MET cc_start: 0.5022 (mtp) cc_final: 0.4744 (mtp) REVERT: G 157 ARG cc_start: 0.6759 (mtm-85) cc_final: 0.6302 (mtp85) REVERT: G 228 PHE cc_start: 0.6979 (t80) cc_final: 0.6408 (t80) REVERT: G 241 LYS cc_start: 0.6918 (tptp) cc_final: 0.6460 (mttp) REVERT: H 7 MET cc_start: 0.4696 (mtp) cc_final: 0.4391 (mtp) REVERT: H 96 ARG cc_start: 0.6765 (mtm-85) cc_final: 0.6328 (ttm110) outliers start: 39 outliers final: 16 residues processed: 328 average time/residue: 1.5094 time to fit residues: 542.3326 Evaluate side-chains 285 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 267 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.4980 chunk 56 optimal weight: 3.9990 chunk 151 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 181 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 162 optimal weight: 0.7980 chunk 180 optimal weight: 0.8980 chunk 62 optimal weight: 0.6980 chunk 145 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18072 Z= 0.217 Angle : 0.625 7.404 24568 Z= 0.309 Chirality : 0.040 0.243 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.361 59.976 4464 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.18 % Allowed : 11.50 % Favored : 85.32 % 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: 1.41 (0.18), residues: 2016 helix: 1.60 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -1.06 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 217 HIS 0.003 0.001 HIS E 219 PHE 0.020 0.002 PHE B 211 TYR 0.013 0.002 TYR D 34 ARG 0.001 0.000 ARG B 200 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 284 time to evaluate : 2.109 Fit side-chains REVERT: A 7 MET cc_start: 0.4921 (mtp) cc_final: 0.4460 (mtp) REVERT: A 83 ARG cc_start: 0.6055 (ptp-110) cc_final: 0.5829 (ptm160) REVERT: A 227 MET cc_start: 0.7016 (mtm) cc_final: 0.6746 (mtm) REVERT: A 228 PHE cc_start: 0.6752 (t80) cc_final: 0.6044 (t80) REVERT: A 237 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5500 (ttmt) REVERT: A 241 LYS cc_start: 0.6824 (tptp) cc_final: 0.6302 (mtmm) REVERT: B 7 MET cc_start: 0.4727 (mtp) cc_final: 0.4523 (mtp) REVERT: B 215 LYS cc_start: 0.6965 (ttmm) cc_final: 0.6704 (ttmm) REVERT: B 219 HIS cc_start: 0.6677 (m-70) cc_final: 0.6418 (m170) REVERT: B 241 LYS cc_start: 0.6660 (tptp) cc_final: 0.6050 (mtmm) REVERT: C 38 GLU cc_start: 0.7527 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: C 237 LYS cc_start: 0.5938 (OUTLIER) cc_final: 0.5526 (ttmt) REVERT: C 241 LYS cc_start: 0.6770 (tptp) cc_final: 0.6302 (mttp) REVERT: D 7 MET cc_start: 0.4730 (mtp) cc_final: 0.4520 (mtp) REVERT: D 215 LYS cc_start: 0.6964 (ttmm) cc_final: 0.6751 (ttmm) REVERT: D 219 HIS cc_start: 0.6712 (m-70) cc_final: 0.6459 (m170) REVERT: D 241 LYS cc_start: 0.6671 (tptp) cc_final: 0.6055 (mtmm) REVERT: E 7 MET cc_start: 0.4923 (mtp) cc_final: 0.4465 (mtp) REVERT: E 38 GLU cc_start: 0.7536 (OUTLIER) cc_final: 0.6757 (tm-30) REVERT: E 237 LYS cc_start: 0.5940 (OUTLIER) cc_final: 0.5531 (ttmt) REVERT: E 241 LYS cc_start: 0.6765 (tptp) cc_final: 0.6321 (mttp) REVERT: F 7 MET cc_start: 0.4687 (mtp) cc_final: 0.4417 (mtp) REVERT: F 215 LYS cc_start: 0.6964 (ttmm) cc_final: 0.6751 (ttmm) REVERT: F 219 HIS cc_start: 0.6712 (m-70) cc_final: 0.6458 (m170) REVERT: F 241 LYS cc_start: 0.6713 (tptp) cc_final: 0.6100 (mtmm) REVERT: G 7 MET cc_start: 0.4921 (mtp) cc_final: 0.4460 (mtp) REVERT: G 83 ARG cc_start: 0.6055 (ptp-110) cc_final: 0.5829 (ptm160) REVERT: G 227 MET cc_start: 0.7067 (mtm) cc_final: 0.6835 (mtp) REVERT: G 237 LYS cc_start: 0.5913 (OUTLIER) cc_final: 0.5501 (ttmt) REVERT: G 241 LYS cc_start: 0.6825 (tptp) cc_final: 0.6304 (mtmm) REVERT: H 7 MET cc_start: 0.4728 (mtp) cc_final: 0.4528 (mtp) REVERT: H 215 LYS cc_start: 0.6965 (ttmm) cc_final: 0.6750 (ttmm) REVERT: H 219 HIS cc_start: 0.6713 (m-70) cc_final: 0.6460 (m170) REVERT: H 228 PHE cc_start: 0.6846 (t80) cc_final: 0.6603 (t80) outliers start: 57 outliers final: 30 residues processed: 305 average time/residue: 1.5753 time to fit residues: 526.4855 Evaluate side-chains 300 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 264 time to evaluate : 1.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 19 MET Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 173 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 18072 Z= 0.231 Angle : 0.629 7.047 24568 Z= 0.308 Chirality : 0.040 0.234 2728 Planarity : 0.005 0.046 2904 Dihedral : 9.126 56.471 4464 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.01 % Allowed : 12.61 % Favored : 84.38 % 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: 1.88 (0.19), residues: 2016 helix: 1.94 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.91 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 217 HIS 0.003 0.001 HIS C 219 PHE 0.015 0.001 PHE F 137 TYR 0.012 0.002 TYR D 34 ARG 0.001 0.000 ARG F 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 274 time to evaluate : 2.028 Fit side-chains REVERT: A 227 MET cc_start: 0.6951 (mtm) cc_final: 0.6724 (mtm) REVERT: A 228 PHE cc_start: 0.6698 (t80) cc_final: 0.6029 (t80) REVERT: A 237 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.5436 (ttmt) REVERT: A 241 LYS cc_start: 0.6759 (tptp) cc_final: 0.6222 (mtmm) REVERT: B 96 ARG cc_start: 0.6790 (mtm110) cc_final: 0.6281 (ttm110) REVERT: B 157 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.6413 (mtt180) REVERT: B 215 LYS cc_start: 0.6919 (ttmm) cc_final: 0.6633 (ttmm) REVERT: B 219 HIS cc_start: 0.6702 (m-70) cc_final: 0.6376 (m170) REVERT: B 241 LYS cc_start: 0.6694 (tptp) cc_final: 0.6034 (mttt) REVERT: C 38 GLU cc_start: 0.7508 (OUTLIER) cc_final: 0.6762 (tm-30) REVERT: C 237 LYS cc_start: 0.5814 (OUTLIER) cc_final: 0.5438 (ttmt) REVERT: C 241 LYS cc_start: 0.6748 (tptp) cc_final: 0.6310 (mtmm) REVERT: D 96 ARG cc_start: 0.6792 (mtm110) cc_final: 0.6281 (ttm110) REVERT: D 157 ARG cc_start: 0.6795 (mtm-85) cc_final: 0.6415 (mtt180) REVERT: D 215 LYS cc_start: 0.6923 (ttmm) cc_final: 0.6687 (ttmm) REVERT: D 219 HIS cc_start: 0.6736 (m-70) cc_final: 0.6416 (m170) REVERT: D 241 LYS cc_start: 0.6698 (tptp) cc_final: 0.6087 (mtmm) REVERT: E 38 GLU cc_start: 0.7507 (OUTLIER) cc_final: 0.6764 (tm-30) REVERT: E 237 LYS cc_start: 0.5823 (OUTLIER) cc_final: 0.5445 (ttmt) REVERT: E 241 LYS cc_start: 0.6736 (tptp) cc_final: 0.6296 (mtmm) REVERT: F 7 MET cc_start: 0.4834 (mtp) cc_final: 0.4249 (mpp) REVERT: F 96 ARG cc_start: 0.6794 (mtm110) cc_final: 0.6283 (ttm110) REVERT: F 157 ARG cc_start: 0.6796 (mtm-85) cc_final: 0.6416 (mtt180) REVERT: F 215 LYS cc_start: 0.6916 (ttmm) cc_final: 0.6684 (ttmm) REVERT: F 219 HIS cc_start: 0.6729 (m-70) cc_final: 0.6419 (m170) REVERT: F 241 LYS cc_start: 0.6715 (tptp) cc_final: 0.6137 (mtmm) REVERT: G 237 LYS cc_start: 0.5832 (OUTLIER) cc_final: 0.5442 (ttmt) REVERT: G 241 LYS cc_start: 0.6746 (tptp) cc_final: 0.6211 (mtmm) REVERT: H 96 ARG cc_start: 0.6792 (mtm110) cc_final: 0.6281 (ttm110) REVERT: H 157 ARG cc_start: 0.6797 (mtm-85) cc_final: 0.6417 (mtt180) REVERT: H 215 LYS cc_start: 0.6921 (ttmm) cc_final: 0.6691 (ttmm) REVERT: H 219 HIS cc_start: 0.6736 (m-70) cc_final: 0.6419 (m170) REVERT: H 228 PHE cc_start: 0.6841 (t80) cc_final: 0.6587 (t80) outliers start: 54 outliers final: 23 residues processed: 304 average time/residue: 1.6272 time to fit residues: 539.4062 Evaluate side-chains 301 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 272 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 143 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 133 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 173 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 18072 Z= 0.273 Angle : 0.662 6.979 24568 Z= 0.320 Chirality : 0.042 0.237 2728 Planarity : 0.005 0.047 2904 Dihedral : 9.414 55.461 4464 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.68 % Allowed : 13.90 % Favored : 83.43 % 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: 1.82 (0.18), residues: 2016 helix: 1.87 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.84 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP E 217 HIS 0.003 0.001 HIS D 219 PHE 0.020 0.002 PHE B 211 TYR 0.013 0.002 TYR F 34 ARG 0.002 0.000 ARG E 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 283 time to evaluate : 1.837 Fit side-chains revert: symmetry clash REVERT: A 157 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6361 (mtp85) REVERT: A 227 MET cc_start: 0.6913 (mtm) cc_final: 0.6700 (mtm) REVERT: A 228 PHE cc_start: 0.6694 (t80) cc_final: 0.6093 (t80) REVERT: A 237 LYS cc_start: 0.5802 (OUTLIER) cc_final: 0.5426 (ttmt) REVERT: A 241 LYS cc_start: 0.6775 (tptp) cc_final: 0.6270 (mttp) REVERT: B 7 MET cc_start: 0.4777 (mtp) cc_final: 0.4381 (mpp) REVERT: B 96 ARG cc_start: 0.6765 (mtm110) cc_final: 0.6289 (ttm110) REVERT: B 215 LYS cc_start: 0.6958 (ttmm) cc_final: 0.6659 (ttmm) REVERT: B 219 HIS cc_start: 0.6759 (m-70) cc_final: 0.6464 (m170) REVERT: B 241 LYS cc_start: 0.6681 (tptp) cc_final: 0.6074 (mtmm) REVERT: C 38 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: C 228 PHE cc_start: 0.6832 (t80) cc_final: 0.6198 (t80) REVERT: C 237 LYS cc_start: 0.5881 (OUTLIER) cc_final: 0.5483 (ttmt) REVERT: C 241 LYS cc_start: 0.6737 (tptp) cc_final: 0.6228 (mtmm) REVERT: D 7 MET cc_start: 0.4735 (mtp) cc_final: 0.4343 (mpp) REVERT: D 96 ARG cc_start: 0.6795 (mtm110) cc_final: 0.6299 (ttm110) REVERT: D 215 LYS cc_start: 0.6964 (ttmm) cc_final: 0.6667 (ttmm) REVERT: D 219 HIS cc_start: 0.6764 (m-70) cc_final: 0.6469 (m170) REVERT: D 241 LYS cc_start: 0.6691 (tptp) cc_final: 0.6075 (mtmm) REVERT: E 38 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.6748 (tm-30) REVERT: E 237 LYS cc_start: 0.5882 (OUTLIER) cc_final: 0.5496 (ttmt) REVERT: E 241 LYS cc_start: 0.6755 (tptp) cc_final: 0.6266 (mtmm) REVERT: F 7 MET cc_start: 0.4817 (mtp) cc_final: 0.4364 (mpp) REVERT: F 96 ARG cc_start: 0.6769 (mtm110) cc_final: 0.6291 (ttm110) REVERT: F 215 LYS cc_start: 0.6966 (ttmm) cc_final: 0.6729 (ttmm) REVERT: F 219 HIS cc_start: 0.6763 (m-70) cc_final: 0.6472 (m170) REVERT: F 241 LYS cc_start: 0.6694 (tptp) cc_final: 0.6095 (mtmm) REVERT: G 157 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6359 (mtp85) REVERT: G 237 LYS cc_start: 0.5794 (OUTLIER) cc_final: 0.5403 (ttmt) REVERT: G 241 LYS cc_start: 0.6774 (tptp) cc_final: 0.6243 (mtmm) REVERT: H 7 MET cc_start: 0.4738 (mtp) cc_final: 0.4353 (mpp) REVERT: H 96 ARG cc_start: 0.6796 (mtm110) cc_final: 0.6315 (ttm110) REVERT: H 215 LYS cc_start: 0.6961 (ttmm) cc_final: 0.6711 (ttmm) REVERT: H 219 HIS cc_start: 0.6772 (m-70) cc_final: 0.6479 (m170) outliers start: 48 outliers final: 30 residues processed: 304 average time/residue: 1.5839 time to fit residues: 526.3583 Evaluate side-chains 310 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 274 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 149 THR Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 134 ILE Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 134 ILE Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 149 THR Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 134 ILE Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 149 THR Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 134 ILE Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.4980 chunk 174 optimal weight: 0.8980 chunk 38 optimal weight: 0.1980 chunk 113 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 chunk 160 optimal weight: 0.0980 chunk 89 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 101 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7041 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 18072 Z= 0.197 Angle : 0.605 7.333 24568 Z= 0.297 Chirality : 0.039 0.222 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.831 54.744 4464 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 2.34 % Allowed : 14.17 % Favored : 83.48 % 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: 2.21 (0.19), residues: 2016 helix: 2.16 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.69 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP C 217 HIS 0.002 0.000 HIS C 219 PHE 0.020 0.001 PHE C 211 TYR 0.011 0.002 TYR E 97 ARG 0.001 0.000 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 2.057 Fit side-chains REVERT: A 7 MET cc_start: 0.4579 (mtp) cc_final: 0.4048 (mpp) REVERT: A 227 MET cc_start: 0.6874 (mtm) cc_final: 0.6428 (mtm) REVERT: A 228 PHE cc_start: 0.6641 (t80) cc_final: 0.6005 (t80) REVERT: A 237 LYS cc_start: 0.5697 (OUTLIER) cc_final: 0.5279 (ttmt) REVERT: A 241 LYS cc_start: 0.6739 (tptp) cc_final: 0.6205 (mtmm) REVERT: B 7 MET cc_start: 0.4819 (mtp) cc_final: 0.4368 (mpp) REVERT: B 96 ARG cc_start: 0.6895 (mtm110) cc_final: 0.6434 (ttm110) REVERT: B 215 LYS cc_start: 0.6854 (ttmm) cc_final: 0.6601 (ttmm) REVERT: B 219 HIS cc_start: 0.6663 (m-70) cc_final: 0.6398 (m170) REVERT: B 241 LYS cc_start: 0.6667 (tptp) cc_final: 0.6002 (ttpp) REVERT: C 7 MET cc_start: 0.4887 (mtp) cc_final: 0.4320 (mpp) REVERT: C 38 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6746 (tm-30) REVERT: C 227 MET cc_start: 0.6809 (mtp) cc_final: 0.6589 (mtp) REVERT: C 237 LYS cc_start: 0.5734 (OUTLIER) cc_final: 0.5307 (ttmt) REVERT: C 241 LYS cc_start: 0.6718 (tptp) cc_final: 0.6207 (mtmm) REVERT: D 7 MET cc_start: 0.4821 (mtp) cc_final: 0.4369 (mpp) REVERT: D 96 ARG cc_start: 0.6898 (mtm110) cc_final: 0.6433 (ttm110) REVERT: D 215 LYS cc_start: 0.6864 (ttmm) cc_final: 0.6605 (mtpm) REVERT: D 219 HIS cc_start: 0.6712 (m-70) cc_final: 0.6457 (m170) REVERT: D 241 LYS cc_start: 0.6694 (tptp) cc_final: 0.6114 (mtmm) REVERT: E 38 GLU cc_start: 0.7479 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: E 223 ILE cc_start: 0.7058 (mm) cc_final: 0.6811 (mp) REVERT: E 237 LYS cc_start: 0.5727 (OUTLIER) cc_final: 0.5310 (ttmt) REVERT: E 241 LYS cc_start: 0.6718 (tptp) cc_final: 0.6223 (mtmm) REVERT: F 7 MET cc_start: 0.4880 (mtp) cc_final: 0.4501 (mpp) REVERT: F 96 ARG cc_start: 0.6897 (mtm110) cc_final: 0.6436 (ttm110) REVERT: F 215 LYS cc_start: 0.6856 (ttmm) cc_final: 0.6599 (mtpm) REVERT: F 219 HIS cc_start: 0.6666 (m-70) cc_final: 0.6409 (m170) REVERT: F 241 LYS cc_start: 0.6699 (tptp) cc_final: 0.6086 (mtmm) REVERT: G 7 MET cc_start: 0.4577 (mtp) cc_final: 0.4050 (mpp) REVERT: G 223 ILE cc_start: 0.7112 (mm) cc_final: 0.6846 (mp) REVERT: G 227 MET cc_start: 0.6859 (mtp) cc_final: 0.6648 (mtm) REVERT: G 237 LYS cc_start: 0.5705 (OUTLIER) cc_final: 0.5299 (ttmt) REVERT: G 241 LYS cc_start: 0.6744 (tptp) cc_final: 0.6221 (mtmm) REVERT: H 7 MET cc_start: 0.4820 (mtp) cc_final: 0.4371 (mpp) REVERT: H 96 ARG cc_start: 0.6835 (mtm110) cc_final: 0.6381 (ttm110) REVERT: H 215 LYS cc_start: 0.6861 (ttmm) cc_final: 0.6652 (ttmm) REVERT: H 219 HIS cc_start: 0.6707 (m-70) cc_final: 0.6444 (m170) outliers start: 42 outliers final: 25 residues processed: 300 average time/residue: 1.6101 time to fit residues: 528.1851 Evaluate side-chains 303 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 272 time to evaluate : 1.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 162 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 192 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 117 optimal weight: 0.5980 chunk 88 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN E 104 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 18072 Z= 0.202 Angle : 0.607 6.730 24568 Z= 0.297 Chirality : 0.039 0.216 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.805 54.743 4464 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.12 % Allowed : 14.45 % Favored : 83.43 % 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: 2.29 (0.19), residues: 2016 helix: 2.20 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.62 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP C 217 HIS 0.003 0.000 HIS F 219 PHE 0.021 0.001 PHE A 211 TYR 0.011 0.002 TYR F 34 ARG 0.002 0.000 ARG E 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 270 time to evaluate : 2.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 MET cc_start: 0.7191 (ttp) cc_final: 0.6977 (ttt) REVERT: A 223 ILE cc_start: 0.7159 (mm) cc_final: 0.6836 (mp) REVERT: A 227 MET cc_start: 0.6885 (mtm) cc_final: 0.6504 (mtm) REVERT: A 237 LYS cc_start: 0.5733 (OUTLIER) cc_final: 0.5382 (ttmt) REVERT: A 241 LYS cc_start: 0.6618 (tptp) cc_final: 0.5973 (mtmm) REVERT: B 7 MET cc_start: 0.4860 (mtp) cc_final: 0.4478 (mpp) REVERT: B 80 GLU cc_start: 0.6950 (tp30) cc_final: 0.6289 (mm-30) REVERT: B 96 ARG cc_start: 0.6824 (mtm110) cc_final: 0.6388 (ttm110) REVERT: B 215 LYS cc_start: 0.6829 (ttmm) cc_final: 0.6626 (ttmm) REVERT: B 219 HIS cc_start: 0.6668 (m-70) cc_final: 0.6429 (m170) REVERT: B 241 LYS cc_start: 0.6705 (tptp) cc_final: 0.6002 (ttpp) REVERT: C 38 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.6755 (tm-30) REVERT: C 227 MET cc_start: 0.6862 (mtp) cc_final: 0.6656 (mtp) REVERT: C 237 LYS cc_start: 0.5788 (OUTLIER) cc_final: 0.5417 (ttmt) REVERT: C 241 LYS cc_start: 0.6583 (tptp) cc_final: 0.5975 (mtmm) REVERT: D 7 MET cc_start: 0.4863 (mtp) cc_final: 0.4477 (mpp) REVERT: D 80 GLU cc_start: 0.6951 (tp30) cc_final: 0.6287 (mm-30) REVERT: D 96 ARG cc_start: 0.6828 (mtm110) cc_final: 0.6388 (ttm110) REVERT: D 215 LYS cc_start: 0.6853 (ttmm) cc_final: 0.6611 (mtpm) REVERT: D 219 HIS cc_start: 0.6678 (m-70) cc_final: 0.6445 (m170) REVERT: D 241 LYS cc_start: 0.6638 (tptp) cc_final: 0.5989 (ttpp) REVERT: E 7 MET cc_start: 0.4798 (mtp) cc_final: 0.4238 (mpp) REVERT: E 38 GLU cc_start: 0.7480 (OUTLIER) cc_final: 0.6724 (tm-30) REVERT: E 237 LYS cc_start: 0.5755 (OUTLIER) cc_final: 0.5381 (ttmt) REVERT: E 241 LYS cc_start: 0.6633 (tptp) cc_final: 0.6040 (mtmm) REVERT: F 7 MET cc_start: 0.4864 (mtp) cc_final: 0.4513 (mpp) REVERT: F 80 GLU cc_start: 0.6954 (tp30) cc_final: 0.6290 (mm-30) REVERT: F 96 ARG cc_start: 0.6828 (mtm110) cc_final: 0.6390 (ttm110) REVERT: F 215 LYS cc_start: 0.6833 (ttmm) cc_final: 0.6588 (mtpm) REVERT: F 219 HIS cc_start: 0.6676 (m-70) cc_final: 0.6448 (m170) REVERT: F 241 LYS cc_start: 0.6692 (tptp) cc_final: 0.6089 (mtmt) REVERT: G 7 MET cc_start: 0.4633 (mtp) cc_final: 0.4189 (mtt) REVERT: G 98 MET cc_start: 0.7192 (ttp) cc_final: 0.6957 (ttt) REVERT: G 223 ILE cc_start: 0.7121 (mm) cc_final: 0.6835 (mp) REVERT: G 237 LYS cc_start: 0.5712 (OUTLIER) cc_final: 0.5330 (ttmt) REVERT: G 241 LYS cc_start: 0.6750 (tptp) cc_final: 0.6203 (mtmm) REVERT: H 7 MET cc_start: 0.4863 (mtp) cc_final: 0.4483 (mpp) REVERT: H 80 GLU cc_start: 0.6948 (tp30) cc_final: 0.6283 (mm-30) REVERT: H 96 ARG cc_start: 0.6831 (mtm110) cc_final: 0.6388 (ttm110) REVERT: H 215 LYS cc_start: 0.6835 (ttmm) cc_final: 0.6587 (mtpm) REVERT: H 219 HIS cc_start: 0.6742 (m-70) cc_final: 0.6514 (m170) outliers start: 38 outliers final: 29 residues processed: 291 average time/residue: 1.6039 time to fit residues: 510.0813 Evaluate side-chains 304 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 269 time to evaluate : 1.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 19 MET Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain E residue 248 PHE Chi-restraints excluded: chain F residue 19 MET Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 19 MET Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 115 optimal weight: 0.0170 chunk 58 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 122 optimal weight: 7.9990 chunk 131 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 151 optimal weight: 0.0070 chunk 175 optimal weight: 10.0000 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 18072 Z= 0.304 Angle : 0.676 6.863 24568 Z= 0.325 Chirality : 0.043 0.224 2728 Planarity : 0.005 0.048 2904 Dihedral : 9.452 55.778 4464 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.34 % Allowed : 14.12 % Favored : 83.54 % 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: 2.02 (0.18), residues: 2016 helix: 1.97 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.59 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP B 217 HIS 0.002 0.001 HIS H 219 PHE 0.019 0.002 PHE E 137 TYR 0.013 0.002 TYR D 34 ARG 0.002 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 295 time to evaluate : 4.533 Fit side-chains REVERT: A 227 MET cc_start: 0.6979 (mtm) cc_final: 0.6606 (mtm) REVERT: A 228 PHE cc_start: 0.6716 (t80) cc_final: 0.6144 (t80) REVERT: A 237 LYS cc_start: 0.5795 (OUTLIER) cc_final: 0.5446 (ttmt) REVERT: A 241 LYS cc_start: 0.6494 (tptp) cc_final: 0.5947 (mtmm) REVERT: B 7 MET cc_start: 0.4874 (mtp) cc_final: 0.4439 (mpp) REVERT: B 96 ARG cc_start: 0.6810 (mtm110) cc_final: 0.6362 (ttm110) REVERT: B 215 LYS cc_start: 0.7010 (ttmm) cc_final: 0.6700 (ttmm) REVERT: B 219 HIS cc_start: 0.6802 (m-70) cc_final: 0.6531 (m90) REVERT: B 241 LYS cc_start: 0.6734 (tptp) cc_final: 0.6023 (ttpp) REVERT: C 38 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.6747 (tm-30) REVERT: C 96 ARG cc_start: 0.6769 (mtt90) cc_final: 0.6381 (ttm110) REVERT: C 227 MET cc_start: 0.7029 (mtp) cc_final: 0.6782 (mtp) REVERT: C 237 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.5445 (ttmt) REVERT: C 241 LYS cc_start: 0.6480 (tptp) cc_final: 0.5936 (mtmm) REVERT: D 7 MET cc_start: 0.4889 (mtp) cc_final: 0.4454 (mpp) REVERT: D 96 ARG cc_start: 0.6814 (mtm110) cc_final: 0.6362 (ttm110) REVERT: D 215 LYS cc_start: 0.7003 (ttmm) cc_final: 0.6745 (ttmm) REVERT: D 219 HIS cc_start: 0.6805 (m-70) cc_final: 0.6537 (m90) REVERT: D 241 LYS cc_start: 0.6654 (tptp) cc_final: 0.5994 (ttpp) REVERT: E 38 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.6750 (tm-30) REVERT: E 237 LYS cc_start: 0.5755 (OUTLIER) cc_final: 0.5409 (ttmt) REVERT: E 241 LYS cc_start: 0.6495 (tptp) cc_final: 0.5934 (mtmm) REVERT: F 7 MET cc_start: 0.4760 (mtp) cc_final: 0.4357 (mpp) REVERT: F 80 GLU cc_start: 0.6996 (tp30) cc_final: 0.6320 (mm-30) REVERT: F 96 ARG cc_start: 0.6815 (mtm110) cc_final: 0.6365 (ttm110) REVERT: F 215 LYS cc_start: 0.6999 (ttmm) cc_final: 0.6739 (ttmm) REVERT: F 219 HIS cc_start: 0.6765 (m-70) cc_final: 0.6489 (m90) REVERT: F 241 LYS cc_start: 0.6719 (tptp) cc_final: 0.6083 (mtmt) REVERT: G 237 LYS cc_start: 0.5850 (OUTLIER) cc_final: 0.5434 (ttmt) REVERT: G 241 LYS cc_start: 0.6642 (tptp) cc_final: 0.6025 (mtmm) REVERT: H 7 MET cc_start: 0.4878 (mtp) cc_final: 0.4445 (mpp) REVERT: H 96 ARG cc_start: 0.6811 (mtm110) cc_final: 0.6506 (ttm110) REVERT: H 215 LYS cc_start: 0.7008 (ttmm) cc_final: 0.6751 (ttmm) REVERT: H 219 HIS cc_start: 0.6809 (m-70) cc_final: 0.6551 (m90) outliers start: 42 outliers final: 28 residues processed: 312 average time/residue: 1.6482 time to fit residues: 571.8863 Evaluate side-chains 320 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 286 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 149 THR Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 38 GLU Chi-restraints excluded: chain C residue 134 ILE Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 19 MET Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 149 THR Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 134 ILE Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 149 THR Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 134 ILE Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 149 THR Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 2.9990 chunk 168 optimal weight: 1.9990 chunk 179 optimal weight: 0.5980 chunk 108 optimal weight: 6.9990 chunk 78 optimal weight: 0.1980 chunk 141 optimal weight: 0.0970 chunk 55 optimal weight: 0.9980 chunk 162 optimal weight: 0.0770 chunk 169 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 189 optimal weight: 0.9990 overall best weight: 0.3336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 GLN C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 GLN E 32 GLN ** E 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 32 GLN F 104 GLN G 32 GLN ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 18072 Z= 0.164 Angle : 0.592 6.712 24568 Z= 0.293 Chirality : 0.038 0.207 2728 Planarity : 0.004 0.048 2904 Dihedral : 8.544 55.158 4464 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.67 % Allowed : 15.85 % Favored : 82.48 % 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: 2.59 (0.19), residues: 2016 helix: 2.40 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.46 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.003 TRP C 217 HIS 0.004 0.001 HIS F 219 PHE 0.026 0.001 PHE A 211 TYR 0.012 0.002 TYR F 97 ARG 0.001 0.000 ARG G 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 295 time to evaluate : 1.878 Fit side-chains REVERT: A 33 MET cc_start: 0.7679 (ttt) cc_final: 0.7020 (ttt) REVERT: A 215 LYS cc_start: 0.6963 (OUTLIER) cc_final: 0.6717 (mtmm) REVERT: A 223 ILE cc_start: 0.7112 (mm) cc_final: 0.6772 (mp) REVERT: A 227 MET cc_start: 0.6766 (mtm) cc_final: 0.6520 (mtm) REVERT: A 228 PHE cc_start: 0.6662 (t80) cc_final: 0.6045 (t80) REVERT: A 237 LYS cc_start: 0.5669 (OUTLIER) cc_final: 0.5290 (tmtt) REVERT: A 241 LYS cc_start: 0.6501 (tptp) cc_final: 0.5998 (ttpp) REVERT: B 7 MET cc_start: 0.4737 (mtp) cc_final: 0.4481 (mpp) REVERT: B 80 GLU cc_start: 0.7138 (tp30) cc_final: 0.6450 (mm-30) REVERT: B 96 ARG cc_start: 0.6818 (mtm110) cc_final: 0.6397 (ttm110) REVERT: B 215 LYS cc_start: 0.6847 (ttmm) cc_final: 0.6596 (ttmm) REVERT: B 241 LYS cc_start: 0.6732 (tptp) cc_final: 0.6033 (ttpp) REVERT: C 7 MET cc_start: 0.4791 (mtp) cc_final: 0.4265 (mpp) REVERT: C 33 MET cc_start: 0.7675 (ttt) cc_final: 0.7012 (ttt) REVERT: C 96 ARG cc_start: 0.6756 (mtt90) cc_final: 0.6358 (ttm110) REVERT: C 227 MET cc_start: 0.6976 (mtp) cc_final: 0.6760 (mtp) REVERT: C 237 LYS cc_start: 0.5608 (OUTLIER) cc_final: 0.5238 (tmtt) REVERT: C 241 LYS cc_start: 0.6511 (tptp) cc_final: 0.5908 (ttpp) REVERT: D 7 MET cc_start: 0.4737 (mtp) cc_final: 0.4463 (mpp) REVERT: D 80 GLU cc_start: 0.7130 (tp30) cc_final: 0.6436 (mm-30) REVERT: D 96 ARG cc_start: 0.6808 (mtm110) cc_final: 0.6533 (ttm110) REVERT: D 215 LYS cc_start: 0.6838 (ttmm) cc_final: 0.6545 (mtpp) REVERT: D 241 LYS cc_start: 0.6590 (tptp) cc_final: 0.5979 (tmmt) REVERT: E 7 MET cc_start: 0.4756 (mtp) cc_final: 0.4175 (mpp) REVERT: E 237 LYS cc_start: 0.5567 (OUTLIER) cc_final: 0.5171 (tmtt) REVERT: E 241 LYS cc_start: 0.6561 (tptp) cc_final: 0.5983 (ttpp) REVERT: F 7 MET cc_start: 0.4746 (mtp) cc_final: 0.4420 (mpp) REVERT: F 80 GLU cc_start: 0.7143 (tp30) cc_final: 0.6437 (mm-30) REVERT: F 96 ARG cc_start: 0.6813 (mtm110) cc_final: 0.6536 (ttm110) REVERT: F 215 LYS cc_start: 0.6824 (ttmm) cc_final: 0.6533 (mtpp) REVERT: F 231 THR cc_start: 0.7557 (m) cc_final: 0.7343 (t) REVERT: F 241 LYS cc_start: 0.6553 (tptp) cc_final: 0.5896 (ttpp) REVERT: G 7 MET cc_start: 0.4727 (mtp) cc_final: 0.4343 (mtt) REVERT: G 33 MET cc_start: 0.7690 (ttt) cc_final: 0.7036 (ttt) REVERT: G 215 LYS cc_start: 0.6910 (ttmm) cc_final: 0.6578 (mtmm) REVERT: G 237 LYS cc_start: 0.5618 (OUTLIER) cc_final: 0.5179 (tmtt) REVERT: G 241 LYS cc_start: 0.6496 (tptp) cc_final: 0.5981 (ttpp) REVERT: H 7 MET cc_start: 0.4739 (mtp) cc_final: 0.4486 (mpp) REVERT: H 80 GLU cc_start: 0.7126 (tp30) cc_final: 0.6431 (mm-30) REVERT: H 96 ARG cc_start: 0.6813 (mtm110) cc_final: 0.6527 (ttm110) REVERT: H 215 LYS cc_start: 0.6865 (ttmm) cc_final: 0.6662 (ttmm) outliers start: 30 outliers final: 24 residues processed: 312 average time/residue: 1.5106 time to fit residues: 516.9157 Evaluate side-chains 305 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 276 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 MET Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 215 LYS Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain B residue 162 ASP Chi-restraints excluded: chain C residue 19 MET Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain C residue 248 PHE Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain D residue 162 ASP Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain E residue 237 LYS Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 162 ASP Chi-restraints excluded: chain G residue 19 MET Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Chi-restraints excluded: chain H residue 162 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.9990 chunk 90 optimal weight: 0.0070 chunk 132 optimal weight: 0.1980 chunk 199 optimal weight: 2.9990 chunk 183 optimal weight: 3.9990 chunk 158 optimal weight: 0.0060 chunk 16 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 97 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 chunk 169 optimal weight: 0.6980 overall best weight: 0.3014 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 219 HIS C 32 GLN C 104 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN D 219 HIS ** E 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 32 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 HIS G 32 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN H 219 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18072 Z= 0.166 Angle : 0.584 6.414 24568 Z= 0.287 Chirality : 0.038 0.199 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.441 56.161 4464 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.28 % Allowed : 16.41 % Favored : 82.31 % 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: 2.75 (0.19), residues: 2016 helix: 2.47 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.24 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP H 217 HIS 0.001 0.000 HIS C 219 PHE 0.025 0.001 PHE A 211 TYR 0.011 0.002 TYR C 247 ARG 0.001 0.000 ARG B 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4032 Ramachandran restraints generated. 2016 Oldfield, 0 Emsley, 2016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 327 time to evaluate : 2.103 Fit side-chains REVERT: A 80 GLU cc_start: 0.7162 (tp30) cc_final: 0.6418 (mm-30) REVERT: A 161 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7273 (tttp) REVERT: A 223 ILE cc_start: 0.7163 (mm) cc_final: 0.6810 (mp) REVERT: A 227 MET cc_start: 0.6739 (mtm) cc_final: 0.6488 (mtm) REVERT: A 228 PHE cc_start: 0.6626 (t80) cc_final: 0.5953 (t80) REVERT: A 234 GLU cc_start: 0.6808 (pt0) cc_final: 0.6197 (tp30) REVERT: A 237 LYS cc_start: 0.5639 (OUTLIER) cc_final: 0.5177 (tmtt) REVERT: B 96 ARG cc_start: 0.6840 (mtm110) cc_final: 0.6378 (ttm110) REVERT: B 157 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.6399 (mtt180) REVERT: B 215 LYS cc_start: 0.6796 (ttmm) cc_final: 0.6529 (ttmm) REVERT: B 219 HIS cc_start: 0.6476 (m-70) cc_final: 0.6254 (m90) REVERT: B 234 GLU cc_start: 0.6878 (pt0) cc_final: 0.6331 (tp30) REVERT: B 241 LYS cc_start: 0.6734 (tptp) cc_final: 0.6068 (ttpp) REVERT: C 7 MET cc_start: 0.4737 (mtp) cc_final: 0.4191 (mpp) REVERT: C 237 LYS cc_start: 0.5645 (OUTLIER) cc_final: 0.5289 (tmtt) REVERT: D 96 ARG cc_start: 0.6841 (mtm110) cc_final: 0.6387 (ttm110) REVERT: D 157 ARG cc_start: 0.6801 (mtm-85) cc_final: 0.6413 (mtt180) REVERT: D 215 LYS cc_start: 0.6755 (ttmm) cc_final: 0.6532 (ttmm) REVERT: D 219 HIS cc_start: 0.6563 (m-70) cc_final: 0.6299 (m90) REVERT: D 234 GLU cc_start: 0.6873 (pt0) cc_final: 0.6331 (tp30) REVERT: D 241 LYS cc_start: 0.6457 (tptp) cc_final: 0.5882 (tmmt) REVERT: E 241 LYS cc_start: 0.6509 (tptp) cc_final: 0.5981 (ttpt) REVERT: F 7 MET cc_start: 0.4665 (mtp) cc_final: 0.4390 (mpp) REVERT: F 96 ARG cc_start: 0.6847 (mtm110) cc_final: 0.6395 (ttm110) REVERT: F 157 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6398 (mtt180) REVERT: F 215 LYS cc_start: 0.6718 (ttmm) cc_final: 0.6453 (mtpp) REVERT: F 241 LYS cc_start: 0.6400 (tptp) cc_final: 0.5908 (tmmt) REVERT: G 80 GLU cc_start: 0.7105 (tp30) cc_final: 0.6364 (mm-30) REVERT: G 161 LYS cc_start: 0.7842 (ttmm) cc_final: 0.7272 (tttp) REVERT: G 215 LYS cc_start: 0.6783 (ttmm) cc_final: 0.6435 (mtmm) REVERT: G 234 GLU cc_start: 0.6792 (pt0) cc_final: 0.6102 (tp30) REVERT: G 237 LYS cc_start: 0.5626 (OUTLIER) cc_final: 0.5283 (ttmt) REVERT: G 241 LYS cc_start: 0.6509 (tptp) cc_final: 0.5947 (mtmm) REVERT: H 96 ARG cc_start: 0.6871 (mtm110) cc_final: 0.6398 (ttm110) REVERT: H 157 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6401 (mtt180) REVERT: H 215 LYS cc_start: 0.6785 (ttmm) cc_final: 0.6559 (ttmm) REVERT: H 219 HIS cc_start: 0.6490 (m-70) cc_final: 0.6272 (m90) REVERT: H 234 GLU cc_start: 0.6733 (pt0) cc_final: 0.6274 (tp30) outliers start: 23 outliers final: 16 residues processed: 340 average time/residue: 1.7301 time to fit residues: 641.3600 Evaluate side-chains 332 residues out of total 1800 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 313 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 LEU Chi-restraints excluded: chain A residue 162 ASP Chi-restraints excluded: chain A residue 237 LYS Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 38 GLU Chi-restraints excluded: chain C residue 28 LEU Chi-restraints excluded: chain C residue 162 ASP Chi-restraints excluded: chain C residue 237 LYS Chi-restraints excluded: chain D residue 28 LEU Chi-restraints excluded: chain D residue 38 GLU Chi-restraints excluded: chain E residue 28 LEU Chi-restraints excluded: chain E residue 162 ASP Chi-restraints excluded: chain F residue 28 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 162 ASP Chi-restraints excluded: chain G residue 237 LYS Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 38 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 6.9990 chunk 146 optimal weight: 0.9980 chunk 23 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 158 optimal weight: 6.9990 chunk 66 optimal weight: 2.9990 chunk 163 optimal weight: 0.0970 chunk 20 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 139 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 32 GLN ** B 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN C 32 GLN ** D 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 32 GLN E 32 GLN ** F 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 219 HIS ** G 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 GLN ** H 20 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 32 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.193936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.119159 restraints weight = 17607.062| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.24 r_work: 0.3040 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18072 Z= 0.198 Angle : 0.619 6.510 24568 Z= 0.304 Chirality : 0.039 0.198 2728 Planarity : 0.004 0.047 2904 Dihedral : 8.581 55.673 4464 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.34 % Allowed : 17.19 % Favored : 81.47 % 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: 2.68 (0.19), residues: 2016 helix: 2.44 (0.13), residues: 1512 sheet: None (None), residues: 0 loop : -0.32 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP C 217 HIS 0.002 0.000 HIS D 219 PHE 0.038 0.001 PHE A 211 TYR 0.012 0.002 TYR D 34 ARG 0.001 0.000 ARG C 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8399.86 seconds wall clock time: 149 minutes 25.63 seconds (8965.63 seconds total)