Starting phenix.real_space_refine on Wed May 21 07:32:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9b05_44029/05_2025/9b05_44029.cif Found real_map, /net/cci-nas-00/data/ceres_data/9b05_44029/05_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_44029/05_2025/9b05_44029.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9b05_44029/05_2025/9b05_44029.map" model { file = "/net/cci-nas-00/data/ceres_data/9b05_44029/05_2025/9b05_44029.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9b05_44029/05_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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/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: 21.32, per 1000 atoms: 1.01 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: 4.90 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: 2.37 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: 6.24 Time building geometry restraints manager: 5.72 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: 0.840 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 57.390 Find NCS groups from input model: 0.840 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.170 ------------------------------------------------------------------------------- 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 : 2.383 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: 1.9694 time to fit residues: 518.2926 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 : 2.523 ------------------------------------------------------------------------------- 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 = 0.075395 restraints weight = 153480.577| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 5.96 r_work: 0.2905 rms_B_bonded: 5.71 restraints_weight: 2.0000 r_work (final): 0.2905 ------------------------------------------------------------------------------- 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: 0.8273 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 14.213 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 0.59515 (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 : 2.297 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: 0.7768 (OUTLIER) cc_final: 0.7114 (tptm) REVERT: A 235 MET cc_start: 0.8633 (ttt) cc_final: 0.8171 (ttp) REVERT: A 339 LYS cc_start: 0.7870 (ptmt) cc_final: 0.7316 (pmmt) REVERT: B 5 ARG cc_start: 0.9094 (mtp-110) cc_final: 0.8894 (mtp180) REVERT: B 265 GLU cc_start: 0.8927 (OUTLIER) cc_final: 0.8669 (mt-10) REVERT: B 339 LYS cc_start: 0.7435 (ptmt) cc_final: 0.7233 (ptpp) REVERT: C 265 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: C 339 LYS cc_start: 0.7702 (ptpt) cc_final: 0.6673 (pmmt) REVERT: D 265 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8671 (mt-10) REVERT: D 339 LYS cc_start: 0.7866 (ptpt) cc_final: 0.7227 (ptpp) REVERT: E 265 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8673 (mt-10) REVERT: E 339 LYS cc_start: 0.7849 (ptmt) cc_final: 0.7540 (ptpp) REVERT: F 265 GLU cc_start: 0.8935 (OUTLIER) cc_final: 0.8691 (mt-10) REVERT: G 265 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8707 (mt-10) REVERT: H 265 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8690 (mt-10) outliers start: 39 outliers final: 6 residues processed: 253 average time/residue: 1.9095 time to fit residues: 530.5279 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 : 2.412 ------------------------------------------------------------------------------- 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: 0.9990 chunk 202 optimal weight: 0.9980 chunk 111 optimal weight: 0.5980 chunk 187 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 256 optimal weight: 10.0000 chunk 151 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 237 optimal weight: 8.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 22 ASN ** 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 = 0.3873 r_free = 0.3873 target = 0.117820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.078918 restraints weight = 139457.362| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 5.85 r_work: 0.2888 rms_B_bonded: 5.67 restraints_weight: 2.0000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2893 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2893 r_free = 0.2893 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2893 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.1107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 21532 Z= 0.121 Angle : 0.580 10.268 29191 Z= 0.283 Chirality : 0.042 0.202 3232 Planarity : 0.006 0.122 3827 Dihedral : 3.788 16.449 3024 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.05 % Allowed : 25.31 % Favored : 73.64 % 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: 0.61 (0.16), residues: 2664 helix: 1.12 (0.16), residues: 1088 sheet: 0.28 (0.25), residues: 320 loop : -0.09 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 213 HIS 0.005 0.001 HIS F 92 PHE 0.019 0.001 PHE B 303 TYR 0.011 0.001 TYR C 95 ARG 0.010 0.000 ARG G 91 Details of bonding type rmsd hydrogen bonds : bond 0.03385 ( 898) hydrogen bonds : angle 4.73404 ( 2507) covalent geometry : bond 0.00280 (21532) covalent geometry : angle 0.57985 (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 235 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 2.489 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: 0.7732 (OUTLIER) cc_final: 0.7509 (tptm) REVERT: A 227 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.8053 (tm-30) REVERT: A 265 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8715 (mt-10) REVERT: A 339 LYS cc_start: 0.7859 (ptmt) cc_final: 0.7333 (pmmt) REVERT: B 5 ARG cc_start: 0.9092 (mtp-110) cc_final: 0.8875 (mtp180) REVERT: B 265 GLU cc_start: 0.8941 (OUTLIER) cc_final: 0.8694 (mt-10) REVERT: B 339 LYS cc_start: 0.7583 (ptmt) cc_final: 0.7372 (ptpp) REVERT: C 4 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7273 (mm-30) REVERT: C 339 LYS cc_start: 0.7624 (ptpt) cc_final: 0.6812 (ptpp) REVERT: D 69 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.6526 (mmt) REVERT: D 265 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8699 (mt-10) REVERT: D 339 LYS cc_start: 0.7775 (ptpt) cc_final: 0.7142 (ptpp) REVERT: E 4 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7267 (mm-30) REVERT: E 265 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8696 (mt-10) REVERT: E 339 LYS cc_start: 0.7735 (ptmt) cc_final: 0.7506 (ptpp) REVERT: F 265 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8713 (mt-10) REVERT: G 265 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8729 (mt-10) REVERT: H 265 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8720 (mt-10) outliers start: 23 outliers final: 4 residues processed: 230 average time/residue: 1.9427 time to fit residues: 490.4415 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 : 2.321 ------------------------------------------------------------------------------- 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 227 GLU Chi-restraints excluded: chain A residue 265 GLU Chi-restraints excluded: chain B residue 265 GLU Chi-restraints excluded: chain D residue 69 MET Chi-restraints excluded: chain D residue 265 GLU Chi-restraints excluded: chain E residue 5 ARG 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: 0.5980 chunk 109 optimal weight: 4.9990 chunk 267 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 211 optimal weight: 0.0470 chunk 137 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 234 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 114 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.1284 ------------------------------------------------------------------------------- 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 = 0.3845 r_free = 0.3845 target = 0.114607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.075257 restraints weight = 155713.735| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 6.12 r_work: 0.2845 rms_B_bonded: 5.75 restraints_weight: 2.0000 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2850 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2850 r_free = 0.2850 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 = 0.2850 r_free = 0.2850 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2850 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21532 Z= 0.172 Angle : 0.602 12.068 29191 Z= 0.296 Chirality : 0.044 0.227 3232 Planarity : 0.005 0.072 3827 Dihedral : 3.888 14.710 3024 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.93 % Allowed : 24.35 % Favored : 73.73 % 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: 0.62 (0.16), residues: 2664 helix: 1.18 (0.16), residues: 1088 sheet: 0.23 (0.24), residues: 320 loop : -0.12 (0.17), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 213 HIS 0.005 0.001 HIS D 92 PHE 0.018 0.001 PHE B 303 TYR 0.013 0.001 TYR C 95 ARG 0.005 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03331 ( 898) hydrogen bonds : angle 4.69168 ( 2507) covalent geometry : bond 0.00409 (21532) covalent geometry : angle 0.60173 (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 253 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 211 time to evaluate : 2.349 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: 0.7739 (OUTLIER) cc_final: 0.7512 (tptm) REVERT: A 265 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8769 (mt-10) REVERT: A 339 LYS cc_start: 0.7903 (ptmt) cc_final: 0.7344 (pmmt) REVERT: C 4 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7325 (mm-30) REVERT: C 339 LYS cc_start: 0.7608 (ptpt) cc_final: 0.6757 (ptpp) REVERT: D 339 LYS cc_start: 0.7859 (ptpt) cc_final: 0.7489 (ptpp) REVERT: E 4 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7339 (mm-30) REVERT: E 265 GLU cc_start: 0.8987 (OUTLIER) cc_final: 0.8773 (mt-10) REVERT: E 339 LYS cc_start: 0.7784 (ptmt) cc_final: 0.7539 (ptpp) REVERT: F 265 GLU cc_start: 0.9000 (OUTLIER) cc_final: 0.8792 (mt-10) REVERT: G 265 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8825 (mt-10) outliers start: 42 outliers final: 12 residues processed: 247 average time/residue: 1.8632 time to fit residues: 505.4555 Evaluate side-chains 228 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 211 time to evaluate : 2.313 ------------------------------------------------------------------------------- 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 A residue 265 GLU Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain D residue 212 ILE 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 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: 9.9990 chunk 208 optimal weight: 4.9990 chunk 95 optimal weight: 0.9990 chunk 254 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 200 optimal weight: 2.9990 chunk 232 optimal weight: 4.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.114342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.075434 restraints weight = 131220.276| |-----------------------------------------------------------------------------| r_work (start): 0.3095 rms_B_bonded: 5.70 r_work: 0.2876 rms_B_bonded: 5.55 restraints_weight: 2.0000 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2885 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2885 r_free = 0.2885 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 = 0.2885 r_free = 0.2885 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2885 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 21532 Z= 0.156 Angle : 0.595 11.411 29191 Z= 0.292 Chirality : 0.043 0.221 3232 Planarity : 0.005 0.070 3827 Dihedral : 3.896 14.353 3024 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.93 % Allowed : 24.53 % 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: 0.70 (0.16), residues: 2664 helix: 1.26 (0.16), residues: 1072 sheet: 0.13 (0.25), residues: 328 loop : -0.03 (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 A 92 PHE 0.019 0.001 PHE G 303 TYR 0.011 0.001 TYR G 95 ARG 0.008 0.000 ARG E 119 Details of bonding type rmsd hydrogen bonds : bond 0.03200 ( 898) hydrogen bonds : angle 4.65620 ( 2507) covalent geometry : bond 0.00371 (21532) covalent geometry : angle 0.59456 (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 250 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 2.516 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: 0.7072 (mm-30) REVERT: A 191 LYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7521 (tptm) REVERT: A 339 LYS cc_start: 0.7882 (ptmt) cc_final: 0.7383 (pmmt) REVERT: B 227 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8125 (tm-30) REVERT: C 4 GLU cc_start: 0.7744 (mm-30) cc_final: 0.7298 (mm-30) REVERT: C 339 LYS cc_start: 0.7654 (OUTLIER) cc_final: 0.6839 (ptpp) REVERT: D 339 LYS cc_start: 0.7866 (ptpt) cc_final: 0.7486 (ptpp) REVERT: E 4 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7330 (mm-30) REVERT: E 265 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8784 (mt-10) REVERT: E 313 GLN cc_start: 0.7401 (OUTLIER) cc_final: 0.6931 (tm-30) REVERT: E 339 LYS cc_start: 0.7727 (ptmt) cc_final: 0.7513 (ptpp) REVERT: F 265 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.8765 (mt-10) REVERT: G 240 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8430 (t0) REVERT: H 240 ASN cc_start: 0.8732 (OUTLIER) cc_final: 0.8428 (t0) outliers start: 42 outliers final: 12 residues processed: 240 average time/residue: 1.9233 time to fit residues: 507.4657 Evaluate side-chains 224 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 204 time to evaluate : 2.408 ------------------------------------------------------------------------------- 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 B residue 212 ILE Chi-restraints excluded: chain B residue 227 GLU 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 265 GLU Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 290 VAL Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 290 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 227 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 220 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 chunk 207 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 208 optimal weight: 0.0980 chunk 64 optimal weight: 8.9990 chunk 164 optimal weight: 10.0000 chunk 160 optimal weight: 3.9990 chunk 177 optimal weight: 0.1980 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3860 r_free = 0.3860 target = 0.115068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.076275 restraints weight = 123352.569| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 5.59 r_work: 0.2898 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 21532 Z= 0.123 Angle : 0.592 12.575 29191 Z= 0.286 Chirality : 0.043 0.245 3232 Planarity : 0.005 0.062 3827 Dihedral : 3.828 14.608 3024 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.65 % Allowed : 25.26 % 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: 0.65 (0.16), residues: 2664 helix: 1.25 (0.16), residues: 1088 sheet: 0.17 (0.25), residues: 328 loop : -0.14 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 213 HIS 0.005 0.001 HIS G 214 PHE 0.041 0.001 PHE E 303 TYR 0.010 0.001 TYR E 95 ARG 0.005 0.000 ARG E 119 Details of bonding type rmsd hydrogen bonds : bond 0.03018 ( 898) hydrogen bonds : angle 4.55620 ( 2507) covalent geometry : bond 0.00288 (21532) covalent geometry : angle 0.59209 (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 240 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 204 time to evaluate : 2.432 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: 0.7558 (mm-30) cc_final: 0.7092 (mm-30) REVERT: A 339 LYS cc_start: 0.7860 (ptmt) cc_final: 0.7399 (pmmt) REVERT: B 240 ASN cc_start: 0.8664 (OUTLIER) cc_final: 0.8393 (t0) REVERT: C 4 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7293 (mm-30) REVERT: C 339 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.6936 (ptpp) REVERT: D 313 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7083 (tm-30) REVERT: D 339 LYS cc_start: 0.7937 (ptpt) cc_final: 0.7236 (pmmt) REVERT: E 4 GLU cc_start: 0.7714 (mm-30) cc_final: 0.7260 (mm-30) REVERT: E 265 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8758 (mt-10) REVERT: E 313 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.7047 (tm-30) REVERT: F 240 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8422 (t0) REVERT: F 265 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8740 (mt-10) REVERT: G 240 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8444 (t0) REVERT: H 240 ASN cc_start: 0.8747 (OUTLIER) cc_final: 0.8430 (t0) REVERT: H 313 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7304 (tm-30) outliers start: 36 outliers final: 6 residues processed: 235 average time/residue: 1.8638 time to fit residues: 480.9041 Evaluate side-chains 216 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 2.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 240 ASN 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 313 GLN Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 265 GLU 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 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 Chi-restraints excluded: chain H residue 313 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 38 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 9.9990 chunk 245 optimal weight: 3.9990 chunk 253 optimal weight: 8.9990 chunk 261 optimal weight: 9.9990 chunk 238 optimal weight: 2.9990 chunk 234 optimal weight: 0.4980 chunk 224 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 313 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3847 r_free = 0.3847 target = 0.114211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075718 restraints weight = 138525.635| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 5.70 r_work: 0.2866 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 21532 Z= 0.157 Angle : 0.608 13.528 29191 Z= 0.294 Chirality : 0.043 0.227 3232 Planarity : 0.005 0.060 3827 Dihedral : 3.899 14.815 3024 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.65 % Allowed : 25.26 % 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: 0.63 (0.16), residues: 2664 helix: 1.24 (0.16), residues: 1088 sheet: 0.15 (0.24), residues: 328 loop : -0.15 (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 C 214 PHE 0.019 0.001 PHE G 303 TYR 0.012 0.001 TYR C 95 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.03137 ( 898) hydrogen bonds : angle 4.55560 ( 2507) covalent geometry : bond 0.00373 (21532) covalent geometry : angle 0.60752 (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: 36 poor density : 201 time to evaluate : 2.333 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: 0.7579 (mm-30) cc_final: 0.7108 (mm-30) REVERT: A 339 LYS cc_start: 0.7874 (ptmt) cc_final: 0.7398 (pmmt) REVERT: C 4 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7317 (mm-30) REVERT: C 339 LYS cc_start: 0.7703 (OUTLIER) cc_final: 0.6973 (ptpp) REVERT: D 4 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7245 (mm-30) REVERT: D 339 LYS cc_start: 0.7913 (ptpt) cc_final: 0.7175 (pmmt) REVERT: E 4 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7280 (mm-30) REVERT: E 313 GLN cc_start: 0.7395 (OUTLIER) cc_final: 0.6896 (tm-30) REVERT: F 186 HIS cc_start: 0.7763 (OUTLIER) cc_final: 0.7403 (t-90) REVERT: F 265 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8784 (mt-10) REVERT: G 240 ASN cc_start: 0.8712 (OUTLIER) cc_final: 0.8430 (t0) REVERT: G 265 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8771 (mt-10) REVERT: H 240 ASN cc_start: 0.8715 (OUTLIER) cc_final: 0.8413 (t0) outliers start: 36 outliers final: 15 residues processed: 227 average time/residue: 1.9261 time to fit residues: 478.9994 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 : 2.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A 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 174 MET Chi-restraints excluded: chain D residue 212 ILE Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 174 MET 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 186 HIS Chi-restraints excluded: chain F residue 265 GLU Chi-restraints excluded: chain F residue 290 VAL Chi-restraints excluded: chain G residue 212 ILE Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 265 GLU Chi-restraints excluded: chain H residue 212 ILE Chi-restraints excluded: chain H residue 240 ASN Chi-restraints excluded: chain H residue 290 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 205 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 189 optimal weight: 4.9990 chunk 160 optimal weight: 5.9990 chunk 96 optimal weight: 10.0000 chunk 203 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 chunk 241 optimal weight: 0.9980 chunk 146 optimal weight: 8.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.113865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.075222 restraints weight = 129599.864| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 5.65 r_work: 0.2870 rms_B_bonded: 5.56 restraints_weight: 2.0000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2890 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2890 r_free = 0.2890 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 = 0.2890 r_free = 0.2890 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2890 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 21532 Z= 0.157 Angle : 0.618 12.726 29191 Z= 0.297 Chirality : 0.043 0.232 3232 Planarity : 0.005 0.059 3827 Dihedral : 3.910 14.901 3024 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.38 % Allowed : 25.72 % 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: 0.64 (0.16), residues: 2664 helix: 1.25 (0.16), residues: 1088 sheet: 0.17 (0.25), residues: 328 loop : -0.16 (0.17), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 46 HIS 0.005 0.001 HIS H 214 PHE 0.040 0.002 PHE E 303 TYR 0.011 0.001 TYR H 95 ARG 0.012 0.000 ARG E 119 Details of bonding type rmsd hydrogen bonds : bond 0.03124 ( 898) hydrogen bonds : angle 4.56269 ( 2507) covalent geometry : bond 0.00374 (21532) covalent geometry : angle 0.61795 (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 230 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 2.388 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: 0.7579 (mm-30) cc_final: 0.7079 (mm-30) REVERT: A 339 LYS cc_start: 0.7881 (ptmt) cc_final: 0.7424 (pmmt) REVERT: C 4 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7338 (mm-30) REVERT: C 339 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.6990 (ptpp) REVERT: D 4 GLU cc_start: 0.7759 (mm-30) cc_final: 0.7231 (mm-30) REVERT: D 313 GLN cc_start: 0.7618 (OUTLIER) cc_final: 0.7150 (tm-30) REVERT: D 339 LYS cc_start: 0.7974 (ptpt) cc_final: 0.7238 (pmmt) REVERT: E 4 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7280 (mm-30) REVERT: E 186 HIS cc_start: 0.7611 (OUTLIER) cc_final: 0.7377 (t-90) REVERT: E 313 GLN cc_start: 0.7467 (OUTLIER) cc_final: 0.6954 (tm-30) REVERT: F 186 HIS cc_start: 0.7761 (OUTLIER) cc_final: 0.7412 (t-90) REVERT: F 240 ASN cc_start: 0.8682 (OUTLIER) cc_final: 0.8405 (t0) REVERT: G 240 ASN cc_start: 0.8744 (OUTLIER) cc_final: 0.8446 (t0) REVERT: H 240 ASN cc_start: 0.8671 (OUTLIER) cc_final: 0.8346 (t0) REVERT: H 313 GLN cc_start: 0.7607 (OUTLIER) cc_final: 0.7220 (tm-30) outliers start: 30 outliers final: 14 residues processed: 223 average time/residue: 1.9450 time to fit residues: 478.0066 Evaluate side-chains 221 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 198 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ARG Chi-restraints excluded: chain A residue 212 ILE 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 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 202 MET Chi-restraints excluded: chain E residue 212 ILE 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 290 VAL 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 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: 0.9990 chunk 50 optimal weight: 0.9980 chunk 204 optimal weight: 1.9990 chunk 265 optimal weight: 0.9990 chunk 146 optimal weight: 8.9990 chunk 61 optimal weight: 1.9990 chunk 136 optimal weight: 0.8980 chunk 157 optimal weight: 0.9990 chunk 209 optimal weight: 4.9990 chunk 154 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.115024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.076377 restraints weight = 136749.681| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 5.76 r_work: 0.2905 rms_B_bonded: 5.64 restraints_weight: 2.0000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1720 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= 0.112 Angle : 0.594 12.267 29191 Z= 0.285 Chirality : 0.042 0.234 3232 Planarity : 0.005 0.052 3827 Dihedral : 3.790 15.093 3024 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.24 % Allowed : 25.81 % 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: 0.63 (0.16), residues: 2664 helix: 1.36 (0.17), residues: 1040 sheet: 0.26 (0.25), residues: 328 loop : -0.24 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 213 HIS 0.004 0.001 HIS F 214 PHE 0.019 0.001 PHE G 303 TYR 0.009 0.001 TYR C 95 ARG 0.004 0.000 ARG A 243 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 898) hydrogen bonds : angle 4.47873 ( 2507) covalent geometry : bond 0.00260 (21532) covalent geometry : angle 0.59430 (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 233 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 2.378 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: 0.7590 (mm-30) cc_final: 0.7114 (mm-30) REVERT: A 339 LYS cc_start: 0.7760 (ptmt) cc_final: 0.7409 (pmmt) REVERT: B 186 HIS cc_start: 0.7715 (OUTLIER) cc_final: 0.7383 (t-90) REVERT: B 240 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8392 (t0) REVERT: C 4 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7306 (mm-30) REVERT: C 186 HIS cc_start: 0.7621 (OUTLIER) cc_final: 0.7380 (t-90) REVERT: C 339 LYS cc_start: 0.7769 (OUTLIER) cc_final: 0.7056 (ptpp) REVERT: D 4 GLU cc_start: 0.7692 (mm-30) cc_final: 0.7180 (mm-30) REVERT: D 313 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7283 (tm-30) REVERT: D 339 LYS cc_start: 0.8016 (ptpt) cc_final: 0.7338 (pmmt) REVERT: E 4 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7244 (mm-30) REVERT: E 186 HIS cc_start: 0.7622 (OUTLIER) cc_final: 0.7384 (t-90) REVERT: E 313 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7032 (tm-30) REVERT: F 186 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.7341 (t-90) REVERT: F 240 ASN cc_start: 0.8738 (OUTLIER) cc_final: 0.8421 (t0) REVERT: G 240 ASN cc_start: 0.8719 (OUTLIER) cc_final: 0.8429 (t0) REVERT: H 240 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8351 (t0) REVERT: H 313 GLN cc_start: 0.7606 (OUTLIER) cc_final: 0.7209 (tm-30) outliers start: 27 outliers final: 6 residues processed: 228 average time/residue: 1.8956 time to fit residues: 473.3466 Evaluate side-chains 218 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 2.280 ------------------------------------------------------------------------------- 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 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 313 GLN Chi-restraints excluded: chain E residue 186 HIS Chi-restraints excluded: chain E residue 202 MET 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 290 VAL 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: 3.9990 chunk 164 optimal weight: 9.9990 chunk 221 optimal weight: 8.9990 chunk 101 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 238 optimal weight: 0.7980 chunk 28 optimal weight: 10.0000 chunk 249 optimal weight: 8.9990 chunk 212 optimal weight: 2.9990 chunk 252 optimal weight: 0.8980 overall best weight: 1.3386 ------------------------------------------------------------------------------- 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 = 0.3862 r_free = 0.3862 target = 0.114783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.075977 restraints weight = 133254.809| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 5.72 r_work: 0.2898 rms_B_bonded: 5.59 restraints_weight: 2.0000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 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 = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 21532 Z= 0.129 Angle : 0.614 13.194 29191 Z= 0.294 Chirality : 0.043 0.234 3232 Planarity : 0.005 0.054 3827 Dihedral : 3.810 15.021 3024 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.15 % Allowed : 25.81 % 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: 0.67 (0.16), residues: 2664 helix: 1.40 (0.17), residues: 1040 sheet: 0.22 (0.25), residues: 328 loop : -0.21 (0.16), residues: 1296 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 0.042 0.002 PHE E 303 TYR 0.010 0.001 TYR C 95 ARG 0.007 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.02956 ( 898) hydrogen bonds : angle 4.51536 ( 2507) covalent geometry : bond 0.00309 (21532) covalent geometry : angle 0.61371 (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 223 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 2.427 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: 0.7668 (mm-30) cc_final: 0.7159 (mm-30) REVERT: A 339 LYS cc_start: 0.7712 (ptmt) cc_final: 0.7383 (pmmt) REVERT: B 186 HIS cc_start: 0.7683 (OUTLIER) cc_final: 0.7403 (t-90) REVERT: B 240 ASN cc_start: 0.8690 (OUTLIER) cc_final: 0.8407 (t0) REVERT: C 4 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7326 (mm-30) REVERT: C 69 MET cc_start: 0.7880 (OUTLIER) cc_final: 0.7444 (mmm) REVERT: C 186 HIS cc_start: 0.7620 (OUTLIER) cc_final: 0.7363 (t-90) REVERT: C 339 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7081 (ptpp) REVERT: D 4 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7206 (mm-30) REVERT: D 313 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7272 (tm-30) REVERT: D 339 LYS cc_start: 0.8012 (ptpt) cc_final: 0.7346 (pmmt) REVERT: E 4 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7273 (mm-30) REVERT: E 313 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7098 (tm-30) REVERT: F 186 HIS cc_start: 0.7660 (OUTLIER) cc_final: 0.7372 (t-90) REVERT: F 240 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.8412 (t0) REVERT: G 240 ASN cc_start: 0.8758 (OUTLIER) cc_final: 0.8455 (t0) REVERT: H 240 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8425 (t0) REVERT: H 299 LYS cc_start: 0.7825 (mmtt) cc_final: 0.7339 (mppt) REVERT: H 313 GLN cc_start: 0.7542 (OUTLIER) cc_final: 0.7176 (tm-30) outliers start: 25 outliers final: 8 residues processed: 217 average time/residue: 1.9536 time to fit residues: 463.4749 Evaluate side-chains 218 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 2.283 ------------------------------------------------------------------------------- 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 69 MET Chi-restraints excluded: chain C residue 186 HIS Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 339 LYS Chi-restraints excluded: chain D residue 5 ARG Chi-restraints excluded: chain D residue 174 MET Chi-restraints excluded: chain D residue 313 GLN Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 202 MET Chi-restraints excluded: chain E residue 313 GLN Chi-restraints excluded: chain F residue 186 HIS Chi-restraints excluded: chain F residue 240 ASN 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 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 259 optimal weight: 7.9990 chunk 261 optimal weight: 1.9990 chunk 136 optimal weight: 0.9980 chunk 229 optimal weight: 0.6980 chunk 243 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 262 optimal weight: 0.8980 chunk 247 optimal weight: 10.0000 chunk 81 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 255 optimal weight: 8.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3868 r_free = 0.3868 target = 0.115082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.076219 restraints weight = 150055.879| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 5.94 r_work: 0.2895 rms_B_bonded: 5.74 restraints_weight: 2.0000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2917 r_free = 0.2917 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 21532 Z= 0.118 Angle : 0.615 12.676 29191 Z= 0.293 Chirality : 0.042 0.238 3232 Planarity : 0.005 0.051 3827 Dihedral : 3.781 15.059 3024 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 0.92 % Allowed : 26.09 % Favored : 72.99 % 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: 0.71 (0.16), residues: 2664 helix: 1.45 (0.17), residues: 1040 sheet: 0.26 (0.25), residues: 328 loop : -0.21 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 213 HIS 0.004 0.001 HIS H 214 PHE 0.018 0.001 PHE F 303 TYR 0.009 0.001 TYR C 95 ARG 0.007 0.000 ARG D 91 Details of bonding type rmsd hydrogen bonds : bond 0.02885 ( 898) hydrogen bonds : angle 4.48969 ( 2507) covalent geometry : bond 0.00279 (21532) covalent geometry : angle 0.61513 (29191) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19078.27 seconds wall clock time: 327 minutes 15.37 seconds (19635.37 seconds total)