Starting phenix.real_space_refine on Wed Jun 18 10:29:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b05_44029/06_2025/9b05_44029.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b05_44029/06_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_44029/06_2025/9b05_44029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b05_44029/06_2025/9b05_44029.map" model { file = "/net/cci-nas-00/data/ceres_data/9b05_44029/06_2025/9b05_44029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b05_44029/06_2025/9b05_44029.cif" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 7, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASP:plan': 2, 'GLU:plan': 8, 'ARG:plan': 3} 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: 21.11, per 1000 atoms: 1.00 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: 4.91 Conformation dependent library (CDL) restraints added in 5.0 seconds 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: 2.50 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: 7.30 Time building geometry restraints manager: 5.92 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.170 Set scattering table: 0.200 Process input model: 60.450 Find NCS groups from input model: 1.040 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.990 ------------------------------------------------------------------------------- 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 : 9.88 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (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 TRP 0.009 0.001 TRP F 213 HIS 0.003 0.001 HIS A 214 PHE 0.022 0.001 PHE A 303 TYR 0.009 0.001 TYR F 95 ARG 0.009 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.17923 ( 898) hydrogen bonds : angle 6.94748 ( 2507) covalent geometry : bond 0.00246 (21532) covalent geometry : angle 0.58687 (29191) *********************** 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 : 2.390 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: 2.0106 time to fit residues: 527.9584 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 : 2.627 ------------------------------------------------------------------------------- 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 229 optimal weight: 0.4980 chunk 206 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 213 optimal weight: 0.6980 chunk 82 optimal weight: 0.7980 chunk 129 optimal weight: 0.9990 chunk 158 optimal weight: 10.0000 chunk 247 optimal weight: 0.4980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.113972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.075393 restraints weight = 153480.750| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 5.96 r_work: 0.2906 rms_B_bonded: 5.69 restraints_weight: 2.0000 r_work (final): 0.2906 ------------------------------------------------------------------------------- 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 = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2913 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.0952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 21532 Z= 0.114 Angle : 0.595 8.513 29191 Z= 0.294 Chirality : 0.042 0.213 3232 Planarity : 0.005 0.101 3827 Dihedral : 3.790 14.214 3030 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.79 % Allowed : 25.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.16), residues: 2664 helix: 1.15 (0.16), residues: 1072 sheet: 0.16 (0.25), residues: 328 loop : 0.07 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 213 HIS 0.004 0.001 HIS G 214 PHE 0.045 0.002 PHE D 303 TYR 0.009 0.001 TYR C 95 ARG 0.012 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.03769 ( 898) hydrogen bonds : angle 5.00026 ( 2507) covalent geometry : bond 0.00253 (21532) covalent geometry : angle 0.59516 (29191) *********************** 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 257 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 218 time to evaluate : 2.576 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 191 LYS cc_start: 0.7777 (OUTLIER) cc_final: 0.7127 (tptm) REVERT: A 235 MET cc_start: 0.8630 (ttt) cc_final: 0.8169 (ttp) REVERT: A 339 LYS cc_start: 0.7867 (ptmt) cc_final: 0.7315 (pmmt) REVERT: B 5 ARG cc_start: 0.9091 (mtp-110) cc_final: 0.8889 (mtp180) REVERT: B 265 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: B 339 LYS cc_start: 0.7437 (ptmt) cc_final: 0.7235 (ptpp) REVERT: C 265 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8690 (mt-10) REVERT: C 339 LYS cc_start: 0.7704 (ptpt) cc_final: 0.6674 (pmmt) REVERT: D 265 GLU cc_start: 0.8918 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: D 339 LYS cc_start: 0.7869 (ptpt) cc_final: 0.7231 (ptpp) REVERT: E 265 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (mt-10) REVERT: E 339 LYS cc_start: 0.7847 (ptmt) cc_final: 0.7539 (ptpp) REVERT: F 265 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8689 (mt-10) REVERT: G 265 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: H 265 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8690 (mt-10) outliers start: 39 outliers final: 6 residues processed: 253 average time/residue: 1.9344 time to fit residues: 535.1481 Evaluate side-chains 218 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 204 time to evaluate : 2.535 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain G residue 265 GLU Chi-restraints excluded: chain H residue 265 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 145 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 202 optimal weight: 0.9980 chunk 111 optimal weight: 0.1980 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 256 optimal weight: 10.0000 chunk 151 optimal weight: 9.9990 chunk 64 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.115324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.076486 restraints weight = 138756.244| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 5.80 r_work: 0.2867 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2872 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2872 r_free = 0.2872 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2872 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1082 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= 0.152 Angle : 0.593 9.736 29191 Z= 0.292 Chirality : 0.043 0.211 3232 Planarity : 0.006 0.119 3827 Dihedral : 3.865 15.525 3024 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.47 % Allowed : 25.03 % Favored : 73.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.16), residues: 2664 helix: 1.12 (0.16), residues: 1088 sheet: 0.24 (0.25), residues: 320 loop : -0.10 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 213 HIS 0.005 0.001 HIS G 92 PHE 0.020 0.001 PHE B 303 TYR 0.011 0.001 TYR C 95 ARG 0.007 0.000 ARG G 91 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 898) hydrogen bonds : angle 4.76995 ( 2507) covalent geometry : bond 0.00357 (21532) covalent geometry : angle 0.59340 (29191) *********************** 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 245 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 213 time to evaluate : 2.307 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: A 191 LYS cc_start: 0.7775 (OUTLIER) cc_final: 0.7180 (tptm) REVERT: A 265 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8727 (mt-10) REVERT: A 339 LYS cc_start: 0.7880 (ptmt) cc_final: 0.7316 (pmmt) REVERT: B 5 ARG cc_start: 0.9094 (mtp-110) cc_final: 0.8870 (mtp180) REVERT: B 265 GLU cc_start: 0.8974 (OUTLIER) cc_final: 0.8738 (mt-10) REVERT: C 4 GLU cc_start: 0.7802 (mm-30) cc_final: 0.7310 (mm-30) REVERT: C 265 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8738 (mt-10) REVERT: C 339 LYS cc_start: 0.7622 (ptpt) cc_final: 0.6780 (ptpp) REVERT: D 69 MET cc_start: 0.7819 (OUTLIER) cc_final: 0.6659 (mmt) REVERT: D 265 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8733 (mt-10) REVERT: D 339 LYS cc_start: 0.7795 (ptpt) cc_final: 0.7143 (ptpp) REVERT: E 4 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7292 (mm-30) REVERT: E 265 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8739 (mt-10) REVERT: E 339 LYS cc_start: 0.7786 (ptmt) cc_final: 0.7522 (ptpp) REVERT: F 265 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8755 (mt-10) REVERT: G 265 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8803 (mt-10) REVERT: H 265 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8777 (mt-10) outliers start: 32 outliers final: 10 residues processed: 237 average time/residue: 2.0524 time to fit residues: 532.2265 Evaluate side-chains 225 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 2.561 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 237 LYS Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 265 GLU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 265 GLU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 265 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 133 optimal weight: 7.9990 chunk 109 optimal weight: 3.9990 chunk 267 optimal weight: 0.9990 chunk 131 optimal weight: 4.9990 chunk 211 optimal weight: 0.0470 chunk 137 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 234 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.114860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075767 restraints weight = 155652.711| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 6.12 r_work: 0.2851 rms_B_bonded: 5.79 restraints_weight: 2.0000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2857 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 21532 Z= 0.152 Angle : 0.595 12.185 29191 Z= 0.292 Chirality : 0.044 0.225 3232 Planarity : 0.005 0.075 3827 Dihedral : 3.871 14.151 3024 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.70 % Allowed : 24.76 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2664 helix: 1.20 (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 TRP 0.005 0.001 TRP D 213 HIS 0.005 0.001 HIS D 92 PHE 0.019 0.001 PHE B 303 TYR 0.013 0.001 TYR F 120 ARG 0.005 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 898) hydrogen bonds : angle 4.69649 ( 2507) covalent geometry : bond 0.00361 (21532) covalent geometry : angle 0.59515 (29191) *********************** 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 245 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 208 time to evaluate : 2.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.7667 (OUTLIER) cc_final: 0.7443 (tptm) REVERT: A 265 GLU cc_start: 0.8995 (OUTLIER) cc_final: 0.8785 (mt-10) REVERT: A 339 LYS cc_start: 0.7877 (ptmt) cc_final: 0.7327 (pmmt) REVERT: B 265 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8776 (mt-10) REVERT: C 4 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7300 (mm-30) REVERT: C 339 LYS cc_start: 0.7598 (ptpt) cc_final: 0.6772 (ptpp) REVERT: D 265 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8755 (mt-10) REVERT: D 339 LYS cc_start: 0.7836 (ptpt) cc_final: 0.7229 (ptpp) REVERT: E 4 GLU cc_start: 0.7787 (mm-30) cc_final: 0.7327 (mm-30) REVERT: E 265 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8769 (mt-10) REVERT: E 339 LYS cc_start: 0.7728 (ptmt) cc_final: 0.7491 (ptpp) REVERT: F 265 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8790 (mt-10) REVERT: G 265 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8814 (mt-10) REVERT: H 265 GLU cc_start: 0.9012 (OUTLIER) cc_final: 0.8801 (mt-10) outliers start: 37 outliers final: 9 residues processed: 239 average time/residue: 1.9536 time to fit residues: 511.5899 Evaluate side-chains 222 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 205 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 191 LYS Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 212 ILE Chi-restraints excluded: chain E residue 265 GLU Chi-restraints excluded: chain F residue 212 ILE Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 265 GLU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain H residue 290 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 159 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 253 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 208 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 254 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 200 optimal weight: 0.9990 chunk 232 optimal weight: 9.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** 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 = 0.3836 r_free = 0.3836 target = 0.113439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.074572 restraints weight = 130584.772| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 5.69 r_work: 0.2851 rms_B_bonded: 5.54 restraints_weight: 2.0000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2855 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2855 r_free = 0.2855 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2855 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 21532 Z= 0.183 Angle : 0.604 12.794 29191 Z= 0.298 Chirality : 0.044 0.204 3232 Planarity : 0.005 0.071 3827 Dihedral : 3.955 14.231 3024 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.15 % Allowed : 24.30 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2664 helix: 1.21 (0.16), residues: 1072 sheet: 0.08 (0.24), residues: 328 loop : -0.02 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 46 HIS 0.005 0.001 HIS G 214 PHE 0.019 0.001 PHE G 303 TYR 0.012 0.001 TYR C 95 ARG 0.005 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03326 ( 898) hydrogen bonds : angle 4.68892 ( 2507) covalent geometry : bond 0.00434 (21532) covalent geometry : angle 0.60442 (29191) *********************** 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 258 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 211 time to evaluate : 2.700 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 191 LYS cc_start: 0.7724 (OUTLIER) cc_final: 0.7166 (tptm) REVERT: A 339 LYS cc_start: 0.7888 (ptmt) cc_final: 0.7364 (pmmt) REVERT: B 227 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8109 (tm-30) REVERT: C 4 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7308 (mm-30) REVERT: C 339 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6831 (ptpp) REVERT: D 339 LYS cc_start: 0.7873 (ptpt) cc_final: 0.7484 (ptpp) REVERT: E 4 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7333 (mm-30) REVERT: E 313 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6939 (tm-30) REVERT: E 339 LYS cc_start: 0.7777 (ptmt) cc_final: 0.7545 (ptpp) REVERT: G 240 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8408 (t0) REVERT: H 240 ASN cc_start: 0.8726 (OUTLIER) cc_final: 0.8421 (t0) outliers start: 47 outliers final: 13 residues processed: 247 average time/residue: 1.9425 time to fit residues: 526.5267 Evaluate side-chains 229 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 210 time to evaluate : 2.728 ------------------------------------------------------------------------------- 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 212 ILE Chi-restraints excluded: chain B residue 227 GLU 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 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 171 LEU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 240 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 227 optimal weight: 7.9990 chunk 87 optimal weight: 0.7980 chunk 220 optimal weight: 6.9990 chunk 106 optimal weight: 0.8980 chunk 207 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 208 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 164 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 177 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** 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 = 0.3863 r_free = 0.3863 target = 0.115320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.077155 restraints weight = 124117.825| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 5.49 r_work: 0.2898 rms_B_bonded: 5.47 restraints_weight: 2.0000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2903 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2903 r_free = 0.2903 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 = 0.2903 r_free = 0.2903 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2903 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.1496 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= 0.115 Angle : 0.601 15.005 29191 Z= 0.289 Chirality : 0.043 0.252 3232 Planarity : 0.005 0.061 3827 Dihedral : 3.837 14.474 3024 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.42 % Allowed : 25.63 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.16), residues: 2664 helix: 1.28 (0.16), residues: 1072 sheet: 0.21 (0.24), residues: 328 loop : -0.02 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 213 HIS 0.004 0.001 HIS F 214 PHE 0.019 0.001 PHE B 303 TYR 0.010 0.001 TYR B 95 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03009 ( 898) hydrogen bonds : angle 4.56875 ( 2507) covalent geometry : bond 0.00266 (21532) covalent geometry : angle 0.60082 (29191) *********************** 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 241 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 210 time to evaluate : 2.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7549 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 339 LYS cc_start: 0.7829 (ptmt) cc_final: 0.7370 (pmmt) REVERT: C 4 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7328 (mm-30) REVERT: C 339 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.6960 (ptpp) REVERT: D 339 LYS cc_start: 0.7911 (ptpt) cc_final: 0.7192 (pmmt) REVERT: E 4 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7270 (mm-30) REVERT: E 313 GLN cc_start: 0.7562 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: G 240 ASN cc_start: 0.8691 (OUTLIER) cc_final: 0.8410 (t0) REVERT: H 240 ASN cc_start: 0.8728 (OUTLIER) cc_final: 0.8412 (t0) outliers start: 31 outliers final: 9 residues processed: 234 average time/residue: 2.0151 time to fit residues: 515.8418 Evaluate side-chains 215 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 202 time to evaluate : 2.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain B residue 212 ILE 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 E residue 5 ARG Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 290 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 38 optimal weight: 0.9980 chunk 197 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 45 optimal weight: 9.9990 chunk 245 optimal weight: 4.9990 chunk 253 optimal weight: 10.0000 chunk 261 optimal weight: 10.0000 chunk 238 optimal weight: 2.9990 chunk 234 optimal weight: 4.9990 chunk 224 optimal weight: 1.9990 chunk 160 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.114642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.076033 restraints weight = 138849.260| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 5.80 r_work: 0.2875 rms_B_bonded: 5.62 restraints_weight: 2.0000 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2880 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2880 r_free = 0.2880 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2880 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 21532 Z= 0.137 Angle : 0.599 12.835 29191 Z= 0.289 Chirality : 0.043 0.225 3232 Planarity : 0.005 0.059 3827 Dihedral : 3.851 14.601 3024 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.56 % Allowed : 25.63 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2664 helix: 1.28 (0.16), residues: 1088 sheet: 0.18 (0.24), residues: 328 loop : -0.13 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 213 HIS 0.005 0.001 HIS H 214 PHE 0.018 0.001 PHE F 303 TYR 0.011 0.001 TYR C 95 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 898) hydrogen bonds : angle 4.52353 ( 2507) covalent geometry : bond 0.00322 (21532) covalent geometry : angle 0.59859 (29191) *********************** 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 237 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 203 time to evaluate : 2.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7568 (mm-30) cc_final: 0.7101 (mm-30) REVERT: A 339 LYS cc_start: 0.7846 (ptmt) cc_final: 0.7398 (pmmt) REVERT: B 240 ASN cc_start: 0.8650 (OUTLIER) cc_final: 0.8381 (t0) REVERT: B 265 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8751 (mt-10) REVERT: C 4 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7321 (mm-30) REVERT: C 339 LYS cc_start: 0.7713 (OUTLIER) cc_final: 0.6973 (ptpp) REVERT: D 4 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7211 (mm-30) REVERT: D 265 GLU cc_start: 0.8986 (OUTLIER) cc_final: 0.8765 (mt-10) REVERT: D 313 GLN cc_start: 0.7582 (OUTLIER) cc_final: 0.7100 (tm-30) REVERT: D 339 LYS cc_start: 0.7950 (ptpt) cc_final: 0.7238 (pmmt) REVERT: E 4 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7277 (mm-30) REVERT: E 313 GLN cc_start: 0.7491 (OUTLIER) cc_final: 0.7000 (tm-30) REVERT: F 240 ASN cc_start: 0.8658 (OUTLIER) cc_final: 0.8396 (t0) REVERT: F 265 GLU cc_start: 0.9001 (OUTLIER) cc_final: 0.8753 (mt-10) REVERT: G 240 ASN cc_start: 0.8716 (OUTLIER) cc_final: 0.8422 (t0) REVERT: H 237 LYS cc_start: 0.9450 (mptm) cc_final: 0.8992 (mmmm) REVERT: H 240 ASN cc_start: 0.8739 (OUTLIER) cc_final: 0.8412 (t0) REVERT: H 265 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8792 (mt-10) REVERT: H 313 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7061 (tm-30) outliers start: 34 outliers final: 10 residues processed: 228 average time/residue: 2.1752 time to fit residues: 540.3192 Evaluate side-chains 221 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 199 time to evaluate : 4.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 265 GLU 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 174 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain H residue 290 VAL 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 205 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 96 optimal weight: 8.9990 chunk 203 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 106 optimal weight: 0.9990 chunk 241 optimal weight: 0.9990 chunk 146 optimal weight: 3.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** 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 = 0.3854 r_free = 0.3854 target = 0.114200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.075536 restraints weight = 130469.345| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 5.66 r_work: 0.2890 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 21532 Z= 0.138 Angle : 0.609 12.442 29191 Z= 0.293 Chirality : 0.043 0.235 3232 Planarity : 0.005 0.055 3827 Dihedral : 3.844 15.046 3024 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 1.38 % Allowed : 25.81 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.16), residues: 2664 helix: 1.30 (0.16), residues: 1040 sheet: 0.20 (0.24), residues: 328 loop : -0.25 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 213 HIS 0.005 0.001 HIS F 214 PHE 0.041 0.001 PHE E 303 TYR 0.010 0.001 TYR H 95 ARG 0.006 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.03027 ( 898) hydrogen bonds : angle 4.51944 ( 2507) covalent geometry : bond 0.00327 (21532) covalent geometry : angle 0.60927 (29191) *********************** 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 232 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 202 time to evaluate : 2.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7048 (mm-30) REVERT: A 265 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8755 (mt-10) REVERT: A 339 LYS cc_start: 0.7789 (ptmt) cc_final: 0.7383 (pmmt) REVERT: B 240 ASN cc_start: 0.8638 (OUTLIER) cc_final: 0.8371 (t0) REVERT: B 265 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8741 (mt-10) REVERT: C 4 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7312 (mm-30) REVERT: C 186 HIS cc_start: 0.7641 (OUTLIER) cc_final: 0.7394 (t-90) REVERT: C 339 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.6980 (ptpp) REVERT: D 4 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7198 (mm-30) REVERT: D 265 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8761 (mt-10) REVERT: D 313 GLN cc_start: 0.7622 (OUTLIER) cc_final: 0.7158 (tm-30) REVERT: D 339 LYS cc_start: 0.7986 (ptpt) cc_final: 0.7292 (pmmt) REVERT: E 4 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7265 (mm-30) REVERT: E 186 HIS cc_start: 0.7531 (OUTLIER) cc_final: 0.7274 (t-90) REVERT: E 313 GLN cc_start: 0.7479 (OUTLIER) cc_final: 0.6989 (tm-30) REVERT: F 186 HIS cc_start: 0.7750 (OUTLIER) cc_final: 0.7399 (t-90) REVERT: F 240 ASN cc_start: 0.8686 (OUTLIER) cc_final: 0.8391 (t0) REVERT: F 265 GLU cc_start: 0.8994 (OUTLIER) cc_final: 0.8763 (mt-10) REVERT: H 240 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8404 (t0) REVERT: H 265 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8784 (mt-10) REVERT: H 313 GLN cc_start: 0.7592 (OUTLIER) cc_final: 0.7049 (tm-30) outliers start: 30 outliers final: 8 residues processed: 227 average time/residue: 2.1283 time to fit residues: 530.5938 Evaluate side-chains 223 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 200 time to evaluate : 2.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain C residue 5 ARG 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 265 GLU Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 186 HIS Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 265 GLU Chi-restraints excluded: chain H residue 290 VAL 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 4 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 204 optimal weight: 0.7980 chunk 265 optimal weight: 0.7980 chunk 146 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 136 optimal weight: 0.0770 chunk 157 optimal weight: 0.9990 chunk 209 optimal weight: 3.9990 chunk 154 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 240 ASN ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.115702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.077066 restraints weight = 137287.368| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 5.80 r_work: 0.2923 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 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 = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 21532 Z= 0.104 Angle : 0.597 12.096 29191 Z= 0.286 Chirality : 0.042 0.232 3232 Planarity : 0.005 0.049 3827 Dihedral : 3.725 15.166 3024 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.15 % Allowed : 25.95 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2664 helix: 1.37 (0.17), residues: 1040 sheet: 0.28 (0.25), residues: 328 loop : -0.22 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 213 HIS 0.004 0.001 HIS F 214 PHE 0.018 0.001 PHE G 303 TYR 0.009 0.001 TYR C 95 ARG 0.007 0.000 ARG E 119 Details of bonding type rmsd hydrogen bonds : bond 0.02839 ( 898) hydrogen bonds : angle 4.45517 ( 2507) covalent geometry : bond 0.00237 (21532) covalent geometry : angle 0.59715 (29191) *********************** 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 225 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 2.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7095 (mm-30) REVERT: A 339 LYS cc_start: 0.7653 (ptmt) cc_final: 0.7361 (pmmt) REVERT: B 69 MET cc_start: 0.8030 (mtm) cc_final: 0.6819 (mtm) REVERT: B 186 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7372 (t-90) REVERT: B 240 ASN cc_start: 0.8685 (OUTLIER) cc_final: 0.8390 (t0) REVERT: C 4 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7261 (mm-30) REVERT: C 186 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7352 (t-90) REVERT: C 339 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7066 (ptpp) REVERT: D 313 GLN cc_start: 0.7847 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: D 339 LYS cc_start: 0.8030 (ptpt) cc_final: 0.7360 (pmmt) REVERT: E 4 GLU cc_start: 0.7588 (mm-30) cc_final: 0.7157 (mm-30) REVERT: E 186 HIS cc_start: 0.7591 (OUTLIER) cc_final: 0.7364 (t-90) REVERT: E 313 GLN cc_start: 0.7570 (OUTLIER) cc_final: 0.7067 (tm-30) REVERT: F 186 HIS cc_start: 0.7671 (OUTLIER) cc_final: 0.7346 (t-90) REVERT: F 240 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8402 (t0) REVERT: G 240 ASN cc_start: 0.8774 (OUTLIER) cc_final: 0.8429 (t0) REVERT: H 240 ASN cc_start: 0.8731 (OUTLIER) cc_final: 0.8404 (t0) REVERT: H 313 GLN cc_start: 0.7603 (OUTLIER) cc_final: 0.7211 (tm-30) outliers start: 25 outliers final: 4 residues processed: 222 average time/residue: 1.9414 time to fit residues: 470.9011 Evaluate side-chains 211 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 195 time to evaluate : 2.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 186 HIS Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 240 ASN Chi-restraints excluded: chain C residue 5 ARG 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 186 HIS Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 186 HIS Chi-restraints excluded: chain F residue 240 ASN Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 290 VAL 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 234 optimal weight: 4.9990 chunk 164 optimal weight: 9.9990 chunk 221 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 238 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 252 optimal weight: 0.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 92 HIS ** 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 = 0.3849 r_free = 0.3849 target = 0.113966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.075166 restraints weight = 132665.085| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 5.71 r_work: 0.2871 rms_B_bonded: 5.57 restraints_weight: 2.0000 r_work (final): 0.2871 ------------------------------------------------------------------------------- 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 = 0.45 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 = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 21532 Z= 0.163 Angle : 0.628 12.254 29191 Z= 0.302 Chirality : 0.044 0.258 3232 Planarity : 0.005 0.055 3827 Dihedral : 3.866 15.195 3024 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.87 % Allowed : 26.18 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.16), residues: 2664 helix: 1.38 (0.17), residues: 1040 sheet: 0.19 (0.24), residues: 328 loop : -0.20 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP H 46 HIS 0.007 0.001 HIS G 92 PHE 0.051 0.002 PHE F 303 TYR 0.011 0.001 TYR H 95 ARG 0.006 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.03091 ( 898) hydrogen bonds : angle 4.52846 ( 2507) covalent geometry : bond 0.00389 (21532) covalent geometry : angle 0.62755 (29191) ********************** 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 218 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 199 time to evaluate : 2.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 339 LYS cc_start: 0.7711 (ptmt) cc_final: 0.7336 (pmmt) REVERT: C 4 GLU cc_start: 0.7784 (mm-30) cc_final: 0.7353 (mm-30) REVERT: C 186 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7376 (t-90) REVERT: C 339 LYS cc_start: 0.7709 (OUTLIER) cc_final: 0.7031 (ptpp) REVERT: D 313 GLN cc_start: 0.7659 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: D 339 LYS cc_start: 0.8032 (ptpt) cc_final: 0.7336 (pmmt) REVERT: E 4 GLU cc_start: 0.7680 (mm-30) cc_final: 0.7222 (mm-30) REVERT: E 119 ARG cc_start: 0.9242 (tmm160) cc_final: 0.8929 (tmm160) REVERT: E 313 GLN cc_start: 0.7566 (OUTLIER) cc_final: 0.7063 (tm-30) REVERT: F 186 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.7412 (t-90) REVERT: F 240 ASN cc_start: 0.8689 (OUTLIER) cc_final: 0.8392 (t0) REVERT: H 313 GLN cc_start: 0.7489 (OUTLIER) cc_final: 0.6973 (tm-30) outliers start: 19 outliers final: 7 residues processed: 212 average time/residue: 2.1000 time to fit residues: 484.7496 Evaluate side-chains 211 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 197 time to evaluate : 2.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 MET Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 5 ARG 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 174 MET Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 186 HIS Chi-restraints excluded: chain F residue 240 ASN 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 259 optimal weight: 4.9990 chunk 261 optimal weight: 3.9990 chunk 136 optimal weight: 0.8980 chunk 229 optimal weight: 4.9990 chunk 243 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 262 optimal weight: 0.9990 chunk 247 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 chunk 255 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 92 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 92 HIS ** 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 = 0.3853 r_free = 0.3853 target = 0.113702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.074320 restraints weight = 148588.799| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 6.01 r_work: 0.2871 rms_B_bonded: 5.77 restraints_weight: 2.0000 r_work (final): 0.2871 ------------------------------------------------------------------------------- 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 = 0.47 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: 0.8275 moved from start: 0.1854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 21532 Z= 0.140 Angle : 0.629 12.004 29191 Z= 0.301 Chirality : 0.043 0.244 3232 Planarity : 0.005 0.052 3827 Dihedral : 3.849 15.246 3024 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.83 % Allowed : 26.27 % Favored : 72.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.16), residues: 2664 helix: 1.38 (0.17), residues: 1040 sheet: 0.24 (0.25), residues: 328 loop : -0.20 (0.17), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 213 HIS 0.005 0.001 HIS F 92 PHE 0.052 0.001 PHE F 303 TYR 0.010 0.001 TYR H 95 ARG 0.006 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.02995 ( 898) hydrogen bonds : angle 4.52209 ( 2507) covalent geometry : bond 0.00335 (21532) covalent geometry : angle 0.62903 (29191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20170.05 seconds wall clock time: 345 minutes 22.72 seconds (20722.72 seconds total)