Starting phenix.real_space_refine on Thu Sep 18 23:24:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b05_44029/09_2025/9b05_44029.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b05_44029/09_2025/9b05_44029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9b05_44029/09_2025/9b05_44029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b05_44029/09_2025/9b05_44029.map" model { file = "/net/cci-nas-00/data/ceres_data/9b05_44029/09_2025/9b05_44029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b05_44029/09_2025/9b05_44029.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.026 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 120 5.16 5 C 13204 2.51 5 N 3866 2.21 5 O 3918 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21108 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 2636 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2625 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Conformer: "B" Number of residues, atoms: 340, 2625 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 bond proxies already assigned to first conformer: 2665 Chain: "B" Number of atoms: 2640 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2629 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Conformer: "B" Number of residues, atoms: 340, 2629 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 bond proxies already assigned to first conformer: 2669 Chain: "C" Number of atoms: 2636 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2625 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Conformer: "B" Number of residues, atoms: 340, 2625 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 bond proxies already assigned to first conformer: 2665 Chain: "D" Number of atoms: 2636 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2625 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Conformer: "B" Number of residues, atoms: 340, 2625 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 bond proxies already assigned to first conformer: 2665 Chain: "E" Number of atoms: 2636 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2625 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Conformer: "B" Number of residues, atoms: 340, 2625 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 138 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 bond proxies already assigned to first conformer: 2665 Chain: "F" Number of atoms: 2644 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2633 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Conformer: "B" Number of residues, atoms: 340, 2633 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 bond proxies already assigned to first conformer: 2673 Chain: "G" Number of atoms: 2640 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2629 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 Conformer: "B" Number of residues, atoms: 340, 2629 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 94 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 73 bond proxies already assigned to first conformer: 2669 Chain: "H" Number of atoms: 2640 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2629 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 Conformer: "B" Number of residues, atoms: 340, 2629 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 322} Chain breaks: 4 Unresolved non-hydrogen bonds: 111 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 93 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'HIS:plan': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 77 bond proxies already assigned to first conformer: 2669 Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N AARG A 151 " occ=0.38 ... (20 atoms not shown) pdb=" NH2BARG A 151 " occ=0.62 residue: pdb=" N AARG B 151 " occ=0.39 ... (20 atoms not shown) pdb=" NH2BARG B 151 " occ=0.61 residue: pdb=" N AARG C 151 " occ=0.31 ... (20 atoms not shown) pdb=" NH2BARG C 151 " occ=0.69 residue: pdb=" N AARG D 151 " occ=0.40 ... (20 atoms not shown) pdb=" NH2BARG D 151 " occ=0.60 residue: pdb=" N AARG E 151 " occ=0.32 ... (20 atoms not shown) pdb=" NH2BARG E 151 " occ=0.68 residue: pdb=" N AARG F 151 " occ=0.34 ... (20 atoms not shown) pdb=" NH2BARG F 151 " occ=0.66 residue: pdb=" N AARG G 151 " occ=0.36 ... (20 atoms not shown) pdb=" NH2BARG G 151 " occ=0.64 residue: pdb=" N AARG H 151 " occ=0.35 ... (20 atoms not shown) pdb=" NH2BARG H 151 " occ=0.65 Time building chain proxies: 8.74, per 1000 atoms: 0.41 Number of scatterers: 21108 At special positions: 0 Unit cell: (133, 133, 92.568, 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 120 16.00 O 3918 8.00 N 3866 7.00 C 13204 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 1.72 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5056 Finding SS restraints... Secondary structure from input PDB file: 128 helices and 24 sheets defined 45.9% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 30 through 38 Processing helix chain 'A' and resid 47 through 58 removed outlier: 4.786A pdb=" N THR A 54 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N GLY A 55 " --> pdb=" O CYS A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 92 Proline residue: A 86 - end of helix Processing helix chain 'A' and resid 107 through 111 removed outlier: 4.012A pdb=" N LYS A 110 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ILE A 111 " --> pdb=" O ALA A 108 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 107 through 111' Processing helix chain 'A' and resid 142 through 158 Processing helix chain 'A' and resid 159 through 160 No H-bonds generated for 'chain 'A' and resid 159 through 160' Processing helix chain 'A' and resid 161 through 164 removed outlier: 3.672A pdb=" N LEU A 164 " --> pdb=" O LYS A 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 161 through 164' Processing helix chain 'A' and resid 175 through 185 Processing helix chain 'A' and resid 194 through 201 Processing helix chain 'A' and resid 240 through 262 removed outlier: 3.704A pdb=" N ARG A 262 " --> pdb=" O LEU A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 282 Processing helix chain 'A' and resid 301 through 310 removed outlier: 4.531A pdb=" N LYS A 305 " --> pdb=" O SER A 301 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 357 removed outlier: 3.572A pdb=" N ASP A 357 " --> pdb=" O ASN A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 15 Processing helix chain 'B' and resid 23 through 29 Processing helix chain 'B' and resid 30 through 38 Processing helix chain 'B' and resid 47 through 58 removed outlier: 4.827A pdb=" N THR B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N GLY B 55 " --> pdb=" O CYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 80 through 92 Proline residue: B 86 - end of helix Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.905A pdb=" N LYS B 110 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 159 removed outlier: 3.925A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 7.267A pdb=" N ASP B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 164 " --> pdb=" O LYS B 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 160 through 164' Processing helix chain 'B' and resid 175 through 185 Processing helix chain 'B' and resid 194 through 199 Processing helix chain 'B' and resid 240 through 262 removed outlier: 3.672A pdb=" N ARG B 262 " --> pdb=" O LEU B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 282 Processing helix chain 'B' and resid 302 through 310 Processing helix chain 'B' and resid 340 through 357 removed outlier: 3.579A pdb=" N ASP B 357 " --> pdb=" O ASN B 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 15 Processing helix chain 'C' and resid 23 through 29 Processing helix chain 'C' and resid 30 through 38 Processing helix chain 'C' and resid 47 through 58 removed outlier: 4.804A pdb=" N THR C 54 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N GLY C 55 " --> pdb=" O CYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 92 Proline residue: C 86 - end of helix Processing helix chain 'C' and resid 107 through 111 removed outlier: 4.062A pdb=" N LYS C 110 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 158 Processing helix chain 'C' and resid 159 through 160 No H-bonds generated for 'chain 'C' and resid 159 through 160' Processing helix chain 'C' and resid 161 through 164 removed outlier: 3.583A pdb=" N LEU C 164 " --> pdb=" O LYS C 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 161 through 164' Processing helix chain 'C' and resid 175 through 185 Processing helix chain 'C' and resid 194 through 199 Processing helix chain 'C' and resid 240 through 262 removed outlier: 3.657A pdb=" N ARG C 262 " --> pdb=" O LEU C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 278 through 282 Processing helix chain 'C' and resid 296 through 300 removed outlier: 4.472A pdb=" N ASP C 300 " --> pdb=" O LEU C 296 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 296 through 300' Processing helix chain 'C' and resid 302 through 310 Processing helix chain 'C' and resid 340 through 357 removed outlier: 3.562A pdb=" N ASP C 357 " --> pdb=" O ASN C 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 15 Processing helix chain 'D' and resid 23 through 29 Processing helix chain 'D' and resid 30 through 38 Processing helix chain 'D' and resid 47 through 58 removed outlier: 4.824A pdb=" N THR D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) removed outlier: 5.136A pdb=" N GLY D 55 " --> pdb=" O CYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 80 through 92 Proline residue: D 86 - end of helix Processing helix chain 'D' and resid 107 through 111 removed outlier: 4.052A pdb=" N LYS D 110 " --> pdb=" O ASP D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 158 Processing helix chain 'D' and resid 159 through 160 No H-bonds generated for 'chain 'D' and resid 159 through 160' Processing helix chain 'D' and resid 161 through 164 removed outlier: 3.620A pdb=" N LEU D 164 " --> pdb=" O LYS D 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 161 through 164' Processing helix chain 'D' and resid 172 through 174 No H-bonds generated for 'chain 'D' and resid 172 through 174' Processing helix chain 'D' and resid 175 through 185 Processing helix chain 'D' and resid 194 through 199 Processing helix chain 'D' and resid 240 through 262 removed outlier: 3.703A pdb=" N ARG D 262 " --> pdb=" O LEU D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 278 through 282 Processing helix chain 'D' and resid 301 through 310 removed outlier: 4.522A pdb=" N LYS D 305 " --> pdb=" O SER D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 357 removed outlier: 3.580A pdb=" N ASP D 357 " --> pdb=" O ASN D 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 23 through 29 Processing helix chain 'E' and resid 30 through 38 Processing helix chain 'E' and resid 47 through 58 removed outlier: 4.819A pdb=" N THR E 54 " --> pdb=" O GLN E 50 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N GLY E 55 " --> pdb=" O CYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 75 through 80 Processing helix chain 'E' and resid 80 through 92 Proline residue: E 86 - end of helix Processing helix chain 'E' and resid 107 through 111 removed outlier: 4.065A pdb=" N LYS E 110 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 158 Processing helix chain 'E' and resid 159 through 160 No H-bonds generated for 'chain 'E' and resid 159 through 160' Processing helix chain 'E' and resid 161 through 164 removed outlier: 3.618A pdb=" N LEU E 164 " --> pdb=" O LYS E 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 161 through 164' Processing helix chain 'E' and resid 175 through 185 Processing helix chain 'E' and resid 194 through 199 Processing helix chain 'E' and resid 240 through 262 removed outlier: 3.695A pdb=" N ARG E 262 " --> pdb=" O LEU E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 282 Processing helix chain 'E' and resid 301 through 310 removed outlier: 4.520A pdb=" N LYS E 305 " --> pdb=" O SER E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 359 removed outlier: 3.580A pdb=" N ASP E 357 " --> pdb=" O ASN E 353 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS E 358 " --> pdb=" O TYR E 354 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 15 Processing helix chain 'F' and resid 23 through 29 Processing helix chain 'F' and resid 30 through 38 Processing helix chain 'F' and resid 47 through 58 removed outlier: 4.845A pdb=" N THR F 54 " --> pdb=" O GLN F 50 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N GLY F 55 " --> pdb=" O CYS F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 75 through 80 Processing helix chain 'F' and resid 80 through 92 Proline residue: F 86 - end of helix Processing helix chain 'F' and resid 107 through 111 removed outlier: 4.044A pdb=" N LYS F 110 " --> pdb=" O ASP F 107 " (cutoff:3.500A) Processing helix chain 'F' and resid 142 through 159 removed outlier: 3.925A pdb=" N GLY F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 164 removed outlier: 7.268A pdb=" N ASP F 163 " --> pdb=" O LEU F 160 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU F 164 " --> pdb=" O LYS F 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 160 through 164' Processing helix chain 'F' and resid 175 through 185 Processing helix chain 'F' and resid 194 through 199 Processing helix chain 'F' and resid 240 through 262 removed outlier: 3.669A pdb=" N ARG F 262 " --> pdb=" O LEU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 282 Processing helix chain 'F' and resid 301 through 310 removed outlier: 4.451A pdb=" N LYS F 305 " --> pdb=" O SER F 301 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 359 removed outlier: 3.570A pdb=" N ASP F 357 " --> pdb=" O ASN F 353 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N CYS F 358 " --> pdb=" O TYR F 354 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 15 Processing helix chain 'G' and resid 23 through 29 Processing helix chain 'G' and resid 30 through 38 Processing helix chain 'G' and resid 47 through 58 removed outlier: 4.855A pdb=" N THR G 54 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N GLY G 55 " --> pdb=" O CYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 75 through 80 Processing helix chain 'G' and resid 80 through 92 Proline residue: G 86 - end of helix Processing helix chain 'G' and resid 107 through 111 removed outlier: 4.098A pdb=" N LYS G 110 " --> pdb=" O ASP G 107 " (cutoff:3.500A) Processing helix chain 'G' and resid 142 through 159 removed outlier: 3.923A pdb=" N GLY G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 160 through 164 removed outlier: 7.271A pdb=" N ASP G 163 " --> pdb=" O LEU G 160 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU G 164 " --> pdb=" O LYS G 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 160 through 164' Processing helix chain 'G' and resid 172 through 174 No H-bonds generated for 'chain 'G' and resid 172 through 174' Processing helix chain 'G' and resid 175 through 185 Processing helix chain 'G' and resid 194 through 199 Processing helix chain 'G' and resid 240 through 262 removed outlier: 3.670A pdb=" N ARG G 262 " --> pdb=" O LEU G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 278 through 282 Processing helix chain 'G' and resid 302 through 310 Processing helix chain 'G' and resid 340 through 357 removed outlier: 3.572A pdb=" N ASP G 357 " --> pdb=" O ASN G 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 15 Processing helix chain 'H' and resid 23 through 29 Processing helix chain 'H' and resid 30 through 38 Processing helix chain 'H' and resid 47 through 58 removed outlier: 4.836A pdb=" N THR H 54 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLY H 55 " --> pdb=" O CYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 75 through 80 Processing helix chain 'H' and resid 80 through 92 Proline residue: H 86 - end of helix Processing helix chain 'H' and resid 107 through 111 removed outlier: 4.038A pdb=" N LYS H 110 " --> pdb=" O ASP H 107 " (cutoff:3.500A) Processing helix chain 'H' and resid 142 through 159 removed outlier: 3.941A pdb=" N GLY H 159 " --> pdb=" O ASP H 155 " (cutoff:3.500A) Processing helix chain 'H' and resid 160 through 164 removed outlier: 7.223A pdb=" N ASP H 163 " --> pdb=" O LEU H 160 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU H 164 " --> pdb=" O LYS H 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 160 through 164' Processing helix chain 'H' and resid 172 through 174 No H-bonds generated for 'chain 'H' and resid 172 through 174' Processing helix chain 'H' and resid 175 through 185 Processing helix chain 'H' and resid 194 through 199 Processing helix chain 'H' and resid 240 through 262 removed outlier: 3.716A pdb=" N ARG H 262 " --> pdb=" O LEU H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 278 through 282 Processing helix chain 'H' and resid 302 through 310 removed outlier: 3.587A pdb=" N LEU H 307 " --> pdb=" O PHE H 303 " (cutoff:3.500A) Processing helix chain 'H' and resid 340 through 357 removed outlier: 3.571A pdb=" N ASP H 357 " --> pdb=" O ASN H 353 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 166 through 170 removed outlier: 3.587A pdb=" N GLY A 211 " --> pdb=" O VAL A 224 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N PHE A 220 " --> pdb=" O ASN A 215 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 268 through 269 Processing sheet with id=AA3, first strand: chain 'A' and resid 312 through 314 Processing sheet with id=AA4, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.607A pdb=" N GLY B 211 " --> pdb=" O VAL B 224 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N PHE B 220 " --> pdb=" O ASN B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 268 through 269 Processing sheet with id=AA6, first strand: chain 'B' and resid 312 through 314 Processing sheet with id=AA7, first strand: chain 'C' and resid 166 through 170 removed outlier: 3.614A pdb=" N GLY C 211 " --> pdb=" O VAL C 224 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE C 220 " --> pdb=" O ASN C 215 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 268 through 269 Processing sheet with id=AA9, first strand: chain 'C' and resid 312 through 314 Processing sheet with id=AB1, first strand: chain 'D' and resid 166 through 170 removed outlier: 3.610A pdb=" N GLY D 211 " --> pdb=" O VAL D 224 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N PHE D 220 " --> pdb=" O ASN D 215 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 268 through 269 Processing sheet with id=AB3, first strand: chain 'D' and resid 312 through 314 Processing sheet with id=AB4, first strand: chain 'E' and resid 166 through 170 removed outlier: 3.598A pdb=" N GLY E 211 " --> pdb=" O VAL E 224 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N PHE E 220 " --> pdb=" O ASN E 215 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 268 through 269 Processing sheet with id=AB6, first strand: chain 'E' and resid 312 through 314 Processing sheet with id=AB7, first strand: chain 'F' and resid 166 through 170 removed outlier: 3.632A pdb=" N GLY F 211 " --> pdb=" O VAL F 224 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N PHE F 220 " --> pdb=" O ASN F 215 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 268 through 269 Processing sheet with id=AB9, first strand: chain 'F' and resid 312 through 313 Processing sheet with id=AC1, first strand: chain 'G' and resid 166 through 170 removed outlier: 3.612A pdb=" N GLY G 211 " --> pdb=" O VAL G 224 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N PHE G 220 " --> pdb=" O ASN G 215 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 268 through 269 Processing sheet with id=AC3, first strand: chain 'G' and resid 312 through 313 Processing sheet with id=AC4, first strand: chain 'H' and resid 166 through 170 removed outlier: 3.607A pdb=" N GLY H 211 " --> pdb=" O VAL H 224 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N PHE H 220 " --> pdb=" O ASN H 215 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 268 through 269 Processing sheet with id=AC6, first strand: chain 'H' and resid 312 through 314 898 hydrogen bonds defined for protein. 2507 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: 3.44 Time building geometry restraints manager: 2.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7221 1.34 - 1.46: 3208 1.46 - 1.57: 10919 1.57 - 1.69: 0 1.69 - 1.81: 184 Bond restraints: 21532 Sorted by residual: bond pdb=" C PHE H 303 " pdb=" N PRO H 304 " ideal model delta sigma weight residual 1.335 1.357 -0.023 1.28e-02 6.10e+03 3.12e+00 bond pdb=" CB GLN C 313 " pdb=" CG GLN C 313 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 1.92e+00 bond pdb=" CB GLN B 313 " pdb=" CG GLN B 313 " ideal model delta sigma weight residual 1.520 1.559 -0.039 3.00e-02 1.11e+03 1.66e+00 bond pdb=" CB GLN H 313 " pdb=" CG GLN H 313 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.58e+00 bond pdb=" CB LYS F 299 " pdb=" CG LYS F 299 " ideal model delta sigma weight residual 1.520 1.554 -0.034 3.00e-02 1.11e+03 1.25e+00 ... (remaining 21527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.82: 28702 1.82 - 3.64: 393 3.64 - 5.45: 48 5.45 - 7.27: 31 7.27 - 9.09: 17 Bond angle restraints: 29191 Sorted by residual: angle pdb=" N VAL E 193 " pdb=" CA VAL E 193 " pdb=" C VAL E 193 " ideal model delta sigma weight residual 112.83 108.95 3.88 9.90e-01 1.02e+00 1.54e+01 angle pdb=" CA LYS F 299 " pdb=" CB LYS F 299 " pdb=" CG LYS F 299 " ideal model delta sigma weight residual 114.10 121.53 -7.43 2.00e+00 2.50e-01 1.38e+01 angle pdb=" CA LYS H 299 " pdb=" CB LYS H 299 " pdb=" CG LYS H 299 " ideal model delta sigma weight residual 114.10 121.08 -6.98 2.00e+00 2.50e-01 1.22e+01 angle pdb=" CA GLN H 313 " pdb=" CB GLN H 313 " pdb=" CG GLN H 313 " ideal model delta sigma weight residual 114.10 120.93 -6.83 2.00e+00 2.50e-01 1.17e+01 angle pdb=" N VAL B 193 " pdb=" CA VAL B 193 " pdb=" C VAL B 193 " ideal model delta sigma weight residual 112.29 109.19 3.10 9.40e-01 1.13e+00 1.09e+01 ... (remaining 29186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 11304 17.88 - 35.76: 1105 35.76 - 53.63: 440 53.63 - 71.51: 77 71.51 - 89.39: 27 Dihedral angle restraints: 12953 sinusoidal: 5121 harmonic: 7832 Sorted by residual: dihedral pdb=" CG ARG A 243 " pdb=" CD ARG A 243 " pdb=" NE ARG A 243 " pdb=" CZ ARG A 243 " ideal model delta sinusoidal sigma weight residual 90.00 42.16 47.84 2 1.50e+01 4.44e-03 1.17e+01 dihedral pdb=" CA ASN G 240 " pdb=" CB ASN G 240 " pdb=" CG ASN G 240 " pdb=" OD1 ASN G 240 " ideal model delta sinusoidal sigma weight residual 120.00 -165.71 -74.29 2 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASN F 240 " pdb=" CB ASN F 240 " pdb=" CG ASN F 240 " pdb=" OD1 ASN F 240 " ideal model delta sinusoidal sigma weight residual 120.00 -165.76 -74.24 2 2.00e+01 2.50e-03 1.11e+01 ... (remaining 12950 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1913 0.029 - 0.059: 856 0.059 - 0.088: 272 0.088 - 0.117: 176 0.117 - 0.146: 15 Chirality restraints: 3232 Sorted by residual: chirality pdb=" CB ILE H 259 " pdb=" CA ILE H 259 " pdb=" CG1 ILE H 259 " pdb=" CG2 ILE H 259 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.36e-01 chirality pdb=" CB ILE F 259 " pdb=" CA ILE F 259 " pdb=" CG1 ILE F 259 " pdb=" CG2 ILE F 259 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CB ILE G 259 " pdb=" CA ILE G 259 " pdb=" CG1 ILE G 259 " pdb=" CG2 ILE G 259 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.14 2.00e-01 2.50e+01 5.09e-01 ... (remaining 3229 not shown) Planarity restraints: 3827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 137 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO E 138 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 138 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 138 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU C 137 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO C 138 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO C 138 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO C 138 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 137 " -0.031 5.00e-02 4.00e+02 4.59e-02 3.37e+00 pdb=" N PRO D 138 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO D 138 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO D 138 " -0.025 5.00e-02 4.00e+02 ... (remaining 3824 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3264 2.76 - 3.29: 19934 3.29 - 3.83: 36370 3.83 - 4.36: 43831 4.36 - 4.90: 74543 Nonbonded interactions: 177942 Sorted by model distance: nonbonded pdb=" O ARG D 204 " pdb=" NH2 ARG D 210 " model vdw 2.224 3.120 nonbonded pdb=" O ARG G 204 " pdb=" NH2 ARG G 210 " model vdw 2.226 3.120 nonbonded pdb=" O ARG B 204 " pdb=" NH2 ARG B 210 " model vdw 2.227 3.120 nonbonded pdb=" O ARG C 204 " pdb=" NH2 ARG C 210 " model vdw 2.228 3.120 nonbonded pdb=" O ARG A 204 " pdb=" NH2 ARG A 210 " model vdw 2.231 3.120 ... (remaining 177937 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 3 through 150 or resid 152 through 359)) selection = (chain 'B' and (resid 3 through 150 or resid 152 through 235 or (resid 236 and ( \ name N or name CA or name C or name O or name CB )) or resid 237 through 359)) selection = (chain 'C' and (resid 3 through 150 or resid 152 through 359)) selection = (chain 'D' and (resid 3 through 150 or resid 152 through 359)) selection = (chain 'E' and (resid 3 through 150 or resid 152 through 359)) selection = (chain 'F' and (resid 3 through 150 or resid 152 through 235 or (resid 236 and ( \ name N or name CA or name C or name O or name CB )) or resid 237 through 298 or \ (resid 299 and (name N or name CA or name C or name O or name CB )) or resid 300 \ through 359)) selection = (chain 'G' and (resid 3 through 150 or resid 152 through 235 or (resid 236 and ( \ name N or name CA or name C or name O or name CB )) or resid 237 through 359)) selection = (chain 'H' and (resid 3 through 150 or resid 152 through 298 or (resid 299 and ( \ name N or name CA or name C or name O or name CB )) or resid 300 through 359)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.31 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: 1.080 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: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 23.590 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 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:6.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 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 : 0.002 0.042 21532 Z= 0.109 Angle : 0.587 9.090 29191 Z= 0.297 Chirality : 0.041 0.146 3232 Planarity : 0.004 0.046 3827 Dihedral : 16.938 89.390 7897 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 0.64 % Allowed : 26.27 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.16), residues: 2664 helix: 0.88 (0.16), residues: 1048 sheet: 0.26 (0.26), residues: 320 loop : 0.10 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 243 TYR 0.009 0.001 TYR F 95 PHE 0.022 0.001 PHE A 303 TRP 0.009 0.001 TRP F 213 HIS 0.003 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00246 (21532) covalent geometry : angle 0.58687 (29191) hydrogen bonds : bond 0.17923 ( 898) hydrogen bonds : angle 6.94748 ( 2507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 228 time to evaluate : 0.648 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: A 339 LYS cc_start: 0.7795 (ptmt) cc_final: 0.7254 (pmmt) REVERT: B 339 LYS cc_start: 0.7470 (ptmt) cc_final: 0.7229 (ptpp) REVERT: C 339 LYS cc_start: 0.7702 (ptpt) cc_final: 0.6694 (pmmt) REVERT: D 339 LYS cc_start: 0.7845 (ptpt) cc_final: 0.7046 (pmmt) REVERT: E 339 LYS cc_start: 0.7906 (ptmt) cc_final: 0.7622 (ptpp) REVERT: F 69 MET cc_start: 0.9397 (mtp) cc_final: 0.9170 (mtt) REVERT: F 339 LYS cc_start: 0.7591 (ptpt) cc_final: 0.6715 (pmmt) REVERT: G 69 MET cc_start: 0.9394 (mtp) cc_final: 0.9189 (mtt) REVERT: H 339 LYS cc_start: 0.7443 (ptmt) cc_final: 0.7236 (ptpp) outliers start: 14 outliers final: 3 residues processed: 241 average time/residue: 0.9562 time to fit residues: 249.8365 Evaluate side-chains 211 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain D residue 23 ASN Chi-restraints excluded: chain E residue 23 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 261 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 7.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN C 240 ASN D 240 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.110241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071586 restraints weight = 144117.979| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 5.78 r_work: 0.2819 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 21532 Z= 0.264 Angle : 0.659 8.273 29191 Z= 0.331 Chirality : 0.046 0.206 3232 Planarity : 0.006 0.115 3827 Dihedral : 4.114 16.634 3030 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.71 % Allowed : 24.71 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.16), residues: 2664 helix: 1.03 (0.16), residues: 1072 sheet: 0.12 (0.24), residues: 320 loop : 0.06 (0.17), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG D 91 TYR 0.012 0.002 TYR E 95 PHE 0.044 0.002 PHE D 303 TRP 0.006 0.001 TRP D 213 HIS 0.004 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00622 (21532) covalent geometry : angle 0.65913 (29191) hydrogen bonds : bond 0.04370 ( 898) hydrogen bonds : angle 5.16959 ( 2507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 221 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7099 (tptm) REVERT: A 339 LYS cc_start: 0.7928 (ptmt) cc_final: 0.7274 (pmmt) REVERT: B 5 ARG cc_start: 0.9144 (mtp-110) cc_final: 0.8918 (mtp180) REVERT: B 339 LYS cc_start: 0.7541 (ptmt) cc_final: 0.7284 (ptpp) REVERT: C 339 LYS cc_start: 0.7704 (ptpt) cc_final: 0.6613 (pmmt) REVERT: D 69 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7516 (mtt) REVERT: D 339 LYS cc_start: 0.7846 (ptpt) cc_final: 0.6907 (pmmt) REVERT: E 339 LYS cc_start: 0.7910 (ptmt) cc_final: 0.7559 (ptpp) REVERT: F 69 MET cc_start: 0.9499 (OUTLIER) cc_final: 0.9216 (mtt) REVERT: G 69 MET cc_start: 0.9478 (OUTLIER) cc_final: 0.9205 (mtt) REVERT: G 227 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8116 (tm-30) REVERT: H 339 LYS cc_start: 0.7495 (ptmt) cc_final: 0.7174 (ptpp) outliers start: 59 outliers final: 16 residues processed: 266 average time/residue: 0.9359 time to fit residues: 271.3429 Evaluate side-chains 231 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 210 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 202 MET Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 227 GLU Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 202 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 247 optimal weight: 6.9990 chunk 167 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 255 optimal weight: 7.9990 chunk 16 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 268 optimal weight: 2.9990 chunk 188 optimal weight: 2.9990 chunk 224 optimal weight: 0.8980 chunk 62 optimal weight: 9.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.111456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.072998 restraints weight = 143592.104| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 5.77 r_work: 0.2848 rms_B_bonded: 5.60 restraints_weight: 2.0000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2853 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2853 r_free = 0.2853 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2853 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 21532 Z= 0.155 Angle : 0.613 7.997 29191 Z= 0.303 Chirality : 0.043 0.201 3232 Planarity : 0.005 0.072 3827 Dihedral : 3.996 14.852 3024 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.79 % Allowed : 25.58 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.16), residues: 2664 helix: 1.07 (0.16), residues: 1072 sheet: 0.05 (0.25), residues: 328 loop : -0.01 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 243 TYR 0.013 0.001 TYR F 95 PHE 0.042 0.002 PHE E 303 TRP 0.006 0.001 TRP D 213 HIS 0.005 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00362 (21532) covalent geometry : angle 0.61338 (29191) hydrogen bonds : bond 0.03608 ( 898) hydrogen bonds : angle 4.82587 ( 2507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 213 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7255 (mm-30) REVERT: A 191 LYS cc_start: 0.7729 (OUTLIER) cc_final: 0.7150 (tptm) REVERT: A 339 LYS cc_start: 0.7968 (ptmt) cc_final: 0.7326 (pmmt) REVERT: B 5 ARG cc_start: 0.9144 (mtp-110) cc_final: 0.8908 (mtp180) REVERT: C 4 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7358 (mm-30) REVERT: C 339 LYS cc_start: 0.7745 (ptpt) cc_final: 0.6626 (pmmt) REVERT: D 4 GLU cc_start: 0.7769 (mm-30) cc_final: 0.7261 (mm-30) REVERT: D 69 MET cc_start: 0.7992 (OUTLIER) cc_final: 0.6963 (mmt) REVERT: E 4 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7331 (mm-30) REVERT: E 339 LYS cc_start: 0.7886 (ptmt) cc_final: 0.7557 (ptpp) REVERT: F 69 MET cc_start: 0.9456 (mtp) cc_final: 0.9186 (mtt) REVERT: G 69 MET cc_start: 0.9435 (mtp) cc_final: 0.9174 (mtt) outliers start: 39 outliers final: 8 residues processed: 238 average time/residue: 0.9549 time to fit residues: 248.8082 Evaluate side-chains 215 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 205 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain H residue 333 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 78 optimal weight: 8.9990 chunk 264 optimal weight: 2.9990 chunk 229 optimal weight: 0.7980 chunk 51 optimal weight: 10.0000 chunk 145 optimal weight: 9.9990 chunk 192 optimal weight: 0.9990 chunk 221 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 270 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.112095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.074015 restraints weight = 111636.884| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 5.24 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3092 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3092 r_free = 0.3092 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3092 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21532 Z= 0.131 Angle : 0.591 8.837 29191 Z= 0.290 Chirality : 0.043 0.211 3232 Planarity : 0.005 0.062 3827 Dihedral : 3.912 15.185 3024 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.42 % Allowed : 25.72 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.16), residues: 2664 helix: 1.16 (0.16), residues: 1072 sheet: 0.10 (0.25), residues: 328 loop : -0.01 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.013 0.001 TYR F 95 PHE 0.019 0.001 PHE F 303 TRP 0.007 0.001 TRP D 213 HIS 0.005 0.001 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00306 (21532) covalent geometry : angle 0.59143 (29191) hydrogen bonds : bond 0.03245 ( 898) hydrogen bonds : angle 4.66114 ( 2507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7156 (mm-30) cc_final: 0.6650 (mm-30) REVERT: A 191 LYS cc_start: 0.7197 (OUTLIER) cc_final: 0.6877 (tptm) REVERT: A 339 LYS cc_start: 0.7840 (ptmt) cc_final: 0.7344 (pmmt) REVERT: B 227 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7606 (tm-30) REVERT: B 265 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8512 (mt-10) REVERT: C 4 GLU cc_start: 0.7363 (mm-30) cc_final: 0.6838 (mm-30) REVERT: C 339 LYS cc_start: 0.7574 (OUTLIER) cc_final: 0.6785 (ptpp) REVERT: D 4 GLU cc_start: 0.7226 (mm-30) cc_final: 0.6742 (mm-30) REVERT: D 339 LYS cc_start: 0.7747 (ptpp) cc_final: 0.6986 (pmmt) REVERT: E 4 GLU cc_start: 0.7357 (mm-30) cc_final: 0.6847 (mm-30) REVERT: E 313 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7168 (tm-30) REVERT: F 69 MET cc_start: 0.9369 (mtp) cc_final: 0.9039 (mtt) REVERT: F 339 LYS cc_start: 0.7585 (ptpp) cc_final: 0.7163 (ptpp) REVERT: G 69 MET cc_start: 0.9367 (mtp) cc_final: 0.9046 (mtt) outliers start: 31 outliers final: 7 residues processed: 232 average time/residue: 0.9402 time to fit residues: 238.1309 Evaluate side-chains 215 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 203 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 174 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 2 optimal weight: 0.7980 chunk 64 optimal weight: 8.9990 chunk 202 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 174 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 246 optimal weight: 0.6980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.112075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.073643 restraints weight = 133614.378| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 5.64 r_work: 0.2866 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 21532 Z= 0.136 Angle : 0.594 12.322 29191 Z= 0.289 Chirality : 0.043 0.219 3232 Planarity : 0.005 0.057 3827 Dihedral : 3.891 14.558 3024 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.97 % Allowed : 25.22 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.16), residues: 2664 helix: 1.22 (0.16), residues: 1072 sheet: 0.13 (0.25), residues: 328 loop : -0.02 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.011 0.001 TYR C 95 PHE 0.041 0.002 PHE E 303 TRP 0.007 0.001 TRP D 213 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00321 (21532) covalent geometry : angle 0.59402 (29191) hydrogen bonds : bond 0.03149 ( 898) hydrogen bonds : angle 4.61110 ( 2507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 205 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7102 (mm-30) REVERT: A 186 HIS cc_start: 0.7667 (OUTLIER) cc_final: 0.7438 (t-90) REVERT: A 191 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7479 (tptm) REVERT: A 339 LYS cc_start: 0.7951 (ptmt) cc_final: 0.7424 (pmmt) REVERT: B 227 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8142 (tm-30) REVERT: B 265 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8764 (mt-10) REVERT: C 4 GLU cc_start: 0.7809 (mm-30) cc_final: 0.7304 (mm-30) REVERT: C 339 LYS cc_start: 0.7664 (OUTLIER) cc_final: 0.6891 (ptpp) REVERT: D 4 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7222 (mm-30) REVERT: D 339 LYS cc_start: 0.7870 (ptpp) cc_final: 0.7174 (pmmt) REVERT: E 4 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7299 (mm-30) REVERT: F 69 MET cc_start: 0.9415 (mtp) cc_final: 0.9169 (mtt) REVERT: F 339 LYS cc_start: 0.7744 (ptpp) cc_final: 0.7341 (ptpp) REVERT: G 69 MET cc_start: 0.9411 (mtp) cc_final: 0.9168 (mtt) outliers start: 43 outliers final: 10 residues processed: 242 average time/residue: 0.9208 time to fit residues: 244.6490 Evaluate side-chains 219 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 75 optimal weight: 0.0670 chunk 234 optimal weight: 3.9990 chunk 138 optimal weight: 2.9990 chunk 187 optimal weight: 7.9990 chunk 218 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 232 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 overall best weight: 2.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.111085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072256 restraints weight = 145421.673| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 5.80 r_work: 0.2842 rms_B_bonded: 5.65 restraints_weight: 2.0000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2848 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2848 r_free = 0.2848 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2848 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 21532 Z= 0.176 Angle : 0.607 10.734 29191 Z= 0.298 Chirality : 0.044 0.237 3232 Planarity : 0.005 0.057 3827 Dihedral : 3.993 14.842 3024 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.83 % Allowed : 25.31 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.16), residues: 2664 helix: 1.12 (0.16), residues: 1088 sheet: 0.08 (0.24), residues: 328 loop : -0.16 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 243 TYR 0.013 0.001 TYR H 95 PHE 0.043 0.001 PHE E 303 TRP 0.005 0.001 TRP D 213 HIS 0.005 0.001 HIS F 214 Details of bonding type rmsd covalent geometry : bond 0.00417 (21532) covalent geometry : angle 0.60729 (29191) hydrogen bonds : bond 0.03267 ( 898) hydrogen bonds : angle 4.65258 ( 2507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7139 (mm-30) REVERT: A 69 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.7447 (mpp) REVERT: A 186 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7483 (t-90) REVERT: A 191 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.7160 (tptm) REVERT: A 339 LYS cc_start: 0.7987 (ptmt) cc_final: 0.7506 (pmmt) REVERT: B 227 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.8183 (tm-30) REVERT: C 4 GLU cc_start: 0.7816 (mm-30) cc_final: 0.7313 (mm-30) REVERT: C 339 LYS cc_start: 0.7711 (OUTLIER) cc_final: 0.6953 (ptpp) REVERT: D 4 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7309 (mm-30) REVERT: D 313 GLN cc_start: 0.7623 (OUTLIER) cc_final: 0.7154 (tm-30) REVERT: D 339 LYS cc_start: 0.7923 (ptpp) cc_final: 0.7286 (pmmt) REVERT: E 4 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7306 (mm-30) REVERT: E 313 GLN cc_start: 0.7366 (OUTLIER) cc_final: 0.6881 (tm-30) REVERT: F 69 MET cc_start: 0.9431 (OUTLIER) cc_final: 0.9152 (mtt) REVERT: F 339 LYS cc_start: 0.7731 (ptpp) cc_final: 0.7332 (ptpp) REVERT: G 69 MET cc_start: 0.9423 (OUTLIER) cc_final: 0.9154 (mtt) REVERT: H 313 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.7246 (tm-30) outliers start: 40 outliers final: 16 residues processed: 230 average time/residue: 0.9939 time to fit residues: 250.3843 Evaluate side-chains 223 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 186 HIS Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 174 MET Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 290 VAL Chi-restraints excluded: chain H residue 313 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 241 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 234 optimal weight: 5.9990 chunk 227 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 61 optimal weight: 0.9980 chunk 117 optimal weight: 0.0060 chunk 103 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 overall best weight: 2.6002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.112930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.073718 restraints weight = 137807.688| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 5.77 r_work: 0.2838 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 21532 Z= 0.198 Angle : 0.628 12.473 29191 Z= 0.307 Chirality : 0.045 0.233 3232 Planarity : 0.005 0.057 3827 Dihedral : 4.060 14.780 3024 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.02 % Allowed : 25.31 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.16), residues: 2664 helix: 1.09 (0.16), residues: 1088 sheet: 0.07 (0.24), residues: 328 loop : -0.15 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.013 0.001 TYR H 95 PHE 0.019 0.001 PHE G 303 TRP 0.004 0.001 TRP D 213 HIS 0.005 0.001 HIS G 214 Details of bonding type rmsd covalent geometry : bond 0.00472 (21532) covalent geometry : angle 0.62834 (29191) hydrogen bonds : bond 0.03335 ( 898) hydrogen bonds : angle 4.64904 ( 2507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 201 time to evaluate : 0.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7168 (mm-30) REVERT: A 69 MET cc_start: 0.9109 (OUTLIER) cc_final: 0.7434 (mpp) REVERT: A 191 LYS cc_start: 0.7707 (OUTLIER) cc_final: 0.7166 (tptm) REVERT: A 339 LYS cc_start: 0.8002 (ptmt) cc_final: 0.7613 (pmmt) REVERT: B 227 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8211 (tm-30) REVERT: C 4 GLU cc_start: 0.7810 (mm-30) cc_final: 0.7321 (mm-30) REVERT: C 69 MET cc_start: 0.9136 (OUTLIER) cc_final: 0.8058 (mtp) REVERT: C 186 HIS cc_start: 0.7753 (OUTLIER) cc_final: 0.7479 (t-90) REVERT: C 339 LYS cc_start: 0.7745 (OUTLIER) cc_final: 0.6980 (ptpp) REVERT: D 4 GLU cc_start: 0.7823 (mm-30) cc_final: 0.7309 (mm-30) REVERT: D 313 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7053 (tm-30) REVERT: D 339 LYS cc_start: 0.7936 (ptpp) cc_final: 0.7334 (pmmt) REVERT: E 4 GLU cc_start: 0.7812 (mm-30) cc_final: 0.7303 (mm-30) REVERT: E 313 GLN cc_start: 0.7386 (OUTLIER) cc_final: 0.6851 (tm-30) REVERT: F 69 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9182 (mtt) REVERT: F 339 LYS cc_start: 0.7791 (ptpp) cc_final: 0.7409 (ptpp) REVERT: G 69 MET cc_start: 0.9424 (OUTLIER) cc_final: 0.9176 (mtt) REVERT: H 313 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7255 (tm-30) outliers start: 44 outliers final: 17 residues processed: 229 average time/residue: 0.9683 time to fit residues: 241.9826 Evaluate side-chains 225 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 313 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 225 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 111 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 193 optimal weight: 10.0000 chunk 110 optimal weight: 0.8980 chunk 179 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 228 optimal weight: 0.9980 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.109591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.071236 restraints weight = 125377.923| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 5.46 r_work: 0.2828 rms_B_bonded: 5.44 restraints_weight: 2.0000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 21532 Z= 0.236 Angle : 0.653 11.391 29191 Z= 0.321 Chirality : 0.046 0.229 3232 Planarity : 0.005 0.058 3827 Dihedral : 4.220 15.080 3024 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.97 % Allowed : 25.40 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.44 (0.16), residues: 2664 helix: 0.98 (0.16), residues: 1088 sheet: 0.02 (0.24), residues: 328 loop : -0.13 (0.18), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.015 0.001 TYR C 95 PHE 0.019 0.002 PHE F 303 TRP 0.005 0.001 TRP C 46 HIS 0.006 0.001 HIS A 214 Details of bonding type rmsd covalent geometry : bond 0.00558 (21532) covalent geometry : angle 0.65333 (29191) hydrogen bonds : bond 0.03553 ( 898) hydrogen bonds : angle 4.73244 ( 2507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 204 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 191 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7111 (tptm) REVERT: A 339 LYS cc_start: 0.8058 (ptmt) cc_final: 0.7639 (pmmt) REVERT: B 227 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8199 (tm-30) REVERT: C 4 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7393 (mm-30) REVERT: C 69 MET cc_start: 0.9175 (OUTLIER) cc_final: 0.8080 (mtp) REVERT: C 186 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7529 (t-90) REVERT: C 339 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7139 (ptpp) REVERT: D 313 GLN cc_start: 0.7462 (OUTLIER) cc_final: 0.7034 (tm-30) REVERT: D 339 LYS cc_start: 0.7981 (ptpp) cc_final: 0.7346 (pmmt) REVERT: E 313 GLN cc_start: 0.7499 (OUTLIER) cc_final: 0.7186 (tm-30) REVERT: F 69 MET cc_start: 0.9466 (OUTLIER) cc_final: 0.9181 (mtt) REVERT: F 339 LYS cc_start: 0.7916 (ptpp) cc_final: 0.7510 (ptpp) REVERT: G 69 MET cc_start: 0.9442 (OUTLIER) cc_final: 0.9162 (mtt) REVERT: H 313 GLN cc_start: 0.7742 (OUTLIER) cc_final: 0.7404 (tm-30) outliers start: 43 outliers final: 13 residues processed: 230 average time/residue: 0.9914 time to fit residues: 249.2120 Evaluate side-chains 226 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 203 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 333 ASN Chi-restraints excluded: chain C residue 5 ARG Chi-restraints excluded: chain C residue 69 MET Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 69 MET Chi-restraints excluded: chain G residue 69 MET Chi-restraints excluded: chain G residue 202 MET Chi-restraints excluded: chain H residue 313 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 89 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 138 optimal weight: 7.9990 chunk 146 optimal weight: 5.9990 chunk 202 optimal weight: 7.9990 chunk 154 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 215 optimal weight: 8.9990 chunk 213 optimal weight: 1.9990 chunk 217 optimal weight: 0.6980 chunk 44 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.113842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.074656 restraints weight = 148760.398| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 5.98 r_work: 0.2853 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21532 Z= 0.134 Angle : 0.614 11.194 29191 Z= 0.300 Chirality : 0.043 0.258 3232 Planarity : 0.005 0.052 3827 Dihedral : 4.006 15.096 3024 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.47 % Allowed : 25.95 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.16), residues: 2664 helix: 1.14 (0.16), residues: 1040 sheet: 0.14 (0.25), residues: 328 loop : -0.24 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 91 TYR 0.010 0.001 TYR H 95 PHE 0.041 0.002 PHE E 303 TRP 0.007 0.001 TRP D 213 HIS 0.005 0.001 HIS B 214 Details of bonding type rmsd covalent geometry : bond 0.00318 (21532) covalent geometry : angle 0.61382 (29191) hydrogen bonds : bond 0.03129 ( 898) hydrogen bonds : angle 4.61627 ( 2507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 200 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.7851 (mpp) REVERT: A 191 LYS cc_start: 0.7632 (OUTLIER) cc_final: 0.7082 (tptm) REVERT: A 218 LYS cc_start: 0.9178 (OUTLIER) cc_final: 0.8803 (mmtm) REVERT: A 339 LYS cc_start: 0.7948 (ptmt) cc_final: 0.7629 (pmmt) REVERT: B 227 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.8186 (tm-30) REVERT: C 4 GLU cc_start: 0.7866 (mm-30) cc_final: 0.7371 (mm-30) REVERT: C 186 HIS cc_start: 0.7707 (OUTLIER) cc_final: 0.7433 (t-90) REVERT: C 339 LYS cc_start: 0.7744 (OUTLIER) cc_final: 0.7043 (ptpp) REVERT: D 313 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7217 (tm-30) REVERT: D 339 LYS cc_start: 0.7976 (ptpp) cc_final: 0.7465 (pmmt) REVERT: E 313 GLN cc_start: 0.7540 (OUTLIER) cc_final: 0.7013 (tm-30) REVERT: F 69 MET cc_start: 0.9412 (mtp) cc_final: 0.9203 (mtt) REVERT: F 339 LYS cc_start: 0.7851 (ptpp) cc_final: 0.7115 (pmmt) REVERT: G 69 MET cc_start: 0.9391 (mtp) cc_final: 0.9181 (mtt) REVERT: H 313 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7370 (tm-30) outliers start: 32 outliers final: 8 residues processed: 221 average time/residue: 1.0037 time to fit residues: 241.7539 Evaluate side-chains 216 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 69 MET Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain B residue 202 MET Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain H residue 313 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 212 optimal weight: 6.9990 chunk 240 optimal weight: 0.5980 chunk 215 optimal weight: 1.9990 chunk 167 optimal weight: 0.0770 chunk 13 optimal weight: 0.7980 chunk 257 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 56 optimal weight: 0.0570 chunk 201 optimal weight: 4.9990 chunk 172 optimal weight: 4.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.115551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077191 restraints weight = 129826.461| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 5.64 r_work: 0.2922 rms_B_bonded: 5.58 restraints_weight: 2.0000 r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 21532 Z= 0.101 Angle : 0.592 11.356 29191 Z= 0.286 Chirality : 0.042 0.245 3232 Planarity : 0.004 0.045 3827 Dihedral : 3.792 16.597 3024 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.64 % Allowed : 26.59 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.16), residues: 2664 helix: 1.41 (0.17), residues: 1040 sheet: 0.29 (0.25), residues: 328 loop : -0.22 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 91 TYR 0.008 0.001 TYR C 95 PHE 0.019 0.001 PHE B 303 TRP 0.011 0.001 TRP D 213 HIS 0.008 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00229 (21532) covalent geometry : angle 0.59207 (29191) hydrogen bonds : bond 0.02815 ( 898) hydrogen bonds : angle 4.49728 ( 2507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5328 Ramachandran restraints generated. 2664 Oldfield, 0 Emsley, 2664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 201 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7671 (mm-30) cc_final: 0.7131 (mm-30) REVERT: A 191 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7183 (tptm) REVERT: B 227 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8111 (tm-30) REVERT: C 4 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7296 (mm-30) REVERT: C 186 HIS cc_start: 0.7550 (OUTLIER) cc_final: 0.7269 (t-90) REVERT: C 339 LYS cc_start: 0.7737 (OUTLIER) cc_final: 0.7079 (ptpp) REVERT: D 4 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7229 (mm-30) REVERT: D 313 GLN cc_start: 0.7810 (OUTLIER) cc_final: 0.7382 (tm-30) REVERT: D 339 LYS cc_start: 0.7815 (ptpp) cc_final: 0.7534 (pmmt) REVERT: E 4 GLU cc_start: 0.7668 (mm-30) cc_final: 0.7107 (mm-30) REVERT: E 313 GLN cc_start: 0.7527 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: F 299 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7496 (mppt) REVERT: H 299 LYS cc_start: 0.7865 (mmtt) cc_final: 0.7401 (mppt) REVERT: H 313 GLN cc_start: 0.7774 (OUTLIER) cc_final: 0.7240 (tm-30) outliers start: 14 outliers final: 3 residues processed: 210 average time/residue: 1.0487 time to fit residues: 239.9311 Evaluate side-chains 199 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 189 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain H residue 313 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 158 optimal weight: 3.9990 chunk 49 optimal weight: 0.0030 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 201 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 189 optimal weight: 0.2980 chunk 22 optimal weight: 1.9990 chunk 155 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 254 optimal weight: 0.9980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.115669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.076699 restraints weight = 145800.894| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 5.96 r_work: 0.2911 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 21532 Z= 0.101 Angle : 0.592 11.448 29191 Z= 0.285 Chirality : 0.042 0.288 3232 Planarity : 0.004 0.044 3827 Dihedral : 3.729 15.724 3024 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.46 % Allowed : 26.50 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.16), residues: 2664 helix: 1.46 (0.17), residues: 1040 sheet: 0.34 (0.25), residues: 328 loop : -0.23 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 91 TYR 0.007 0.001 TYR H 95 PHE 0.054 0.002 PHE H 303 TRP 0.011 0.001 TRP D 213 HIS 0.004 0.001 HIS B 92 Details of bonding type rmsd covalent geometry : bond 0.00232 (21532) covalent geometry : angle 0.59190 (29191) hydrogen bonds : bond 0.02808 ( 898) hydrogen bonds : angle 4.46465 ( 2507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9884.93 seconds wall clock time: 168 minutes 23.55 seconds (10103.55 seconds total)