Starting phenix.real_space_refine on Tue Jul 29 21:32:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r0o_18799/07_2025/8r0o_18799_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r0o_18799/07_2025/8r0o_18799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r0o_18799/07_2025/8r0o_18799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r0o_18799/07_2025/8r0o_18799.map" model { file = "/net/cci-nas-00/data/ceres_data/8r0o_18799/07_2025/8r0o_18799_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r0o_18799/07_2025/8r0o_18799_neut.cif" } resolution = 2.3 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= 0.017 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 50 5.16 5 C 7643 2.51 5 N 1786 2.21 5 O 2298 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 143 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11777 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 283, 2110 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 Conformer: "B" Number of residues, atoms: 283, 2110 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 39 bond proxies already assigned to first conformer: 2053 Chain: "B" Number of atoms: 2220 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 283, 2118 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 Conformer: "B" Number of residues, atoms: 283, 2118 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 33 bond proxies already assigned to first conformer: 2061 Chain: "C" Number of atoms: 2211 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 283, 2109 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Conformer: "B" Number of residues, atoms: 283, 2109 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 44 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 7, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 bond proxies already assigned to first conformer: 2052 Chain: "D" Number of atoms: 2213 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 283, 2111 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 283, 2111 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 2054 Chain: "E" Number of atoms: 2213 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 283, 2111 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 Conformer: "B" Number of residues, atoms: 283, 2111 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 274} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 38 bond proxies already assigned to first conformer: 2054 Chain: "A" Number of atoms: 73 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 34 Chain: "B" Number of atoms: 73 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 34 Chain: "C" Number of atoms: 73 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 34 Chain: "D" Number of atoms: 73 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 34 Chain: "E" Number of atoms: 73 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 2, 53 Unusual residues: {'LMT': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 34 Chain: "A" Number of atoms: 67 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Conformer: "A" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "B" Number of atoms: 67 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Conformer: "A" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Chain: "C" Number of atoms: 74 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 72, 72 Classifications: {'water': 72} Link IDs: {None: 71} Conformer: "B" Number of residues, atoms: 73, 73 Classifications: {'water': 73} Link IDs: {None: 72} Chain: "D" Number of atoms: 68 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 67, 67 Classifications: {'water': 67} Link IDs: {None: 66} Conformer: "A" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Chain: "E" Number of atoms: 67 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 66, 66 Classifications: {'water': 66} Link IDs: {None: 65} Conformer: "A" Number of residues, atoms: 64, 64 Classifications: {'water': 64} Link IDs: {None: 63} Residues with excluded nonbonded symmetry interactions: 87 residue: pdb=" N AARG A 57 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 57 " occ=0.50 residue: pdb=" N AILE A 201 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 201 " occ=0.50 residue: pdb=" N APHE A 202 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 202 " occ=0.50 residue: pdb=" N ALEU A 203 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 203 " occ=0.50 residue: pdb=" N AMET A 204 " occ=0.50 ... (14 atoms not shown) pdb=" CE BMET A 204 " occ=0.50 residue: pdb=" N ASER A 205 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 205 " occ=0.50 residue: pdb=" N ALYS A 241 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 241 " occ=0.50 residue: pdb=" N ALEU A 242 " occ=0.50 ... (14 atoms not shown) pdb=" CD2BLEU A 242 " occ=0.50 residue: pdb=" N AGLY A 243 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 243 " occ=0.50 residue: pdb=" N APHE A 244 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 244 " occ=0.50 residue: pdb=" N ACYS A 245 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 245 " occ=0.50 residue: pdb=" N AGLY A 246 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 246 " occ=0.50 ... (remaining 75 not shown) Time building chain proxies: 15.35, per 1000 atoms: 1.30 Number of scatterers: 11777 At special positions: 0 Unit cell: (91.96, 90.706, 85.272, 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 50 16.00 O 2298 8.00 N 1786 7.00 C 7643 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=10, symmetry=0 Number of additional bonds: simple=10, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 2.8 seconds 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2720 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 10 sheets defined 81.3% alpha, 4.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 7 through 11 removed outlier: 3.596A pdb=" N ALA A 11 " --> pdb=" O PRO A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 42 Processing helix chain 'A' and resid 43 through 46 removed outlier: 3.562A pdb=" N VAL A 46 " --> pdb=" O ARG A 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 43 through 46' Processing helix chain 'A' and resid 47 through 49 No H-bonds generated for 'chain 'A' and resid 47 through 49' Processing helix chain 'A' and resid 50 through 78 removed outlier: 4.195A pdb=" N VAL A 54 " --> pdb=" O TYR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 96 Processing helix chain 'A' and resid 97 through 117 removed outlier: 3.817A pdb=" N VAL A 101 " --> pdb=" O ALA A 97 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.947A pdb=" N VAL A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 148 Processing helix chain 'A' and resid 155 through 185 Processing helix chain 'A' and resid 186 through 188 No H-bonds generated for 'chain 'A' and resid 186 through 188' Processing helix chain 'A' and resid 189 through 208 removed outlier: 3.620A pdb=" N ALA A 208 " --> pdb=" O BMET A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 209 through 220 removed outlier: 3.933A pdb=" N ALA A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR A 214 " --> pdb=" O TYR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 262 removed outlier: 3.559A pdb=" N BPHE A 244 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N ACYS A 245 " --> pdb=" O ALYS A 241 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N BGLY A 246 " --> pdb=" O BLEU A 242 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N BLEU A 247 " --> pdb=" O BGLY A 243 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE A 248 " --> pdb=" O BPHE A 244 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N HIS A 249 " --> pdb=" O BCYS A 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 11 removed outlier: 3.598A pdb=" N ALA B 11 " --> pdb=" O PRO B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 15 through 42 Processing helix chain 'B' and resid 43 through 46 removed outlier: 3.568A pdb=" N VAL B 46 " --> pdb=" O ARG B 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 46' Processing helix chain 'B' and resid 47 through 49 No H-bonds generated for 'chain 'B' and resid 47 through 49' Processing helix chain 'B' and resid 50 through 78 removed outlier: 4.193A pdb=" N VAL B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 96 Processing helix chain 'B' and resid 97 through 117 removed outlier: 3.815A pdb=" N VAL B 101 " --> pdb=" O ALA B 97 " (cutoff:3.500A) Proline residue: B 108 - end of helix removed outlier: 3.968A pdb=" N VAL B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 148 Processing helix chain 'B' and resid 155 through 185 Processing helix chain 'B' and resid 186 through 188 No H-bonds generated for 'chain 'B' and resid 186 through 188' Processing helix chain 'B' and resid 189 through 208 removed outlier: 3.623A pdb=" N ALA B 208 " --> pdb=" O BMET B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 220 removed outlier: 3.932A pdb=" N ALA B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N TYR B 214 " --> pdb=" O TYR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 262 removed outlier: 3.564A pdb=" N BPHE B 244 " --> pdb=" O VAL B 240 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ACYS B 245 " --> pdb=" O ALYS B 241 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N BGLY B 246 " --> pdb=" O BLEU B 242 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N BLEU B 247 " --> pdb=" O BGLY B 243 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ILE B 248 " --> pdb=" O BPHE B 244 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS B 249 " --> pdb=" O BCYS B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.595A pdb=" N ALA C 11 " --> pdb=" O PRO C 8 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 42 Processing helix chain 'C' and resid 43 through 46 removed outlier: 3.565A pdb=" N VAL C 46 " --> pdb=" O ARG C 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 43 through 46' Processing helix chain 'C' and resid 47 through 49 No H-bonds generated for 'chain 'C' and resid 47 through 49' Processing helix chain 'C' and resid 50 through 78 removed outlier: 4.199A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 97 through 117 removed outlier: 3.816A pdb=" N VAL C 101 " --> pdb=" O ALA C 97 " (cutoff:3.500A) Proline residue: C 108 - end of helix removed outlier: 3.945A pdb=" N VAL C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 148 Processing helix chain 'C' and resid 155 through 185 Processing helix chain 'C' and resid 186 through 188 No H-bonds generated for 'chain 'C' and resid 186 through 188' Processing helix chain 'C' and resid 189 through 208 removed outlier: 3.686A pdb=" N ALA C 208 " --> pdb=" O BMET C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.936A pdb=" N ALA C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N TYR C 214 " --> pdb=" O TYR C 210 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 262 removed outlier: 3.568A pdb=" N BPHE C 244 " --> pdb=" O VAL C 240 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N ACYS C 245 " --> pdb=" O ALYS C 241 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N BGLY C 246 " --> pdb=" O BLEU C 242 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N BLEU C 247 " --> pdb=" O BGLY C 243 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N ILE C 248 " --> pdb=" O BPHE C 244 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N HIS C 249 " --> pdb=" O BCYS C 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 11 removed outlier: 3.598A pdb=" N ALA D 11 " --> pdb=" O PRO D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 42 Processing helix chain 'D' and resid 43 through 46 removed outlier: 3.564A pdb=" N VAL D 46 " --> pdb=" O ARG D 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 43 through 46' Processing helix chain 'D' and resid 47 through 49 No H-bonds generated for 'chain 'D' and resid 47 through 49' Processing helix chain 'D' and resid 50 through 78 removed outlier: 4.190A pdb=" N VAL D 54 " --> pdb=" O TYR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 96 Processing helix chain 'D' and resid 97 through 117 removed outlier: 3.816A pdb=" N VAL D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) Proline residue: D 108 - end of helix removed outlier: 3.968A pdb=" N VAL D 117 " --> pdb=" O GLU D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 148 Processing helix chain 'D' and resid 155 through 185 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 189 through 208 removed outlier: 3.713A pdb=" N ALA D 208 " --> pdb=" O BMET D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 209 through 220 removed outlier: 3.929A pdb=" N ALA D 213 " --> pdb=" O VAL D 209 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR D 214 " --> pdb=" O TYR D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 262 removed outlier: 3.586A pdb=" N BPHE D 244 " --> pdb=" O VAL D 240 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N ACYS D 245 " --> pdb=" O ALYS D 241 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N BGLY D 246 " --> pdb=" O BLEU D 242 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N BLEU D 247 " --> pdb=" O BGLY D 243 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE D 248 " --> pdb=" O BPHE D 244 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N HIS D 249 " --> pdb=" O BCYS D 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 7 through 11 removed outlier: 3.597A pdb=" N ALA E 11 " --> pdb=" O PRO E 8 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 42 Processing helix chain 'E' and resid 43 through 46 removed outlier: 3.567A pdb=" N VAL E 46 " --> pdb=" O ARG E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 43 through 46' Processing helix chain 'E' and resid 47 through 49 No H-bonds generated for 'chain 'E' and resid 47 through 49' Processing helix chain 'E' and resid 50 through 78 removed outlier: 4.203A pdb=" N VAL E 54 " --> pdb=" O TYR E 50 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 96 Processing helix chain 'E' and resid 97 through 117 removed outlier: 3.817A pdb=" N VAL E 101 " --> pdb=" O ALA E 97 " (cutoff:3.500A) Proline residue: E 108 - end of helix removed outlier: 3.967A pdb=" N VAL E 117 " --> pdb=" O GLU E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 148 Processing helix chain 'E' and resid 155 through 185 Processing helix chain 'E' and resid 186 through 188 No H-bonds generated for 'chain 'E' and resid 186 through 188' Processing helix chain 'E' and resid 189 through 208 removed outlier: 3.741A pdb=" N ALA E 208 " --> pdb=" O BMET E 204 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 220 removed outlier: 3.931A pdb=" N ALA E 213 " --> pdb=" O VAL E 209 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N TYR E 214 " --> pdb=" O TYR E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 262 removed outlier: 3.575A pdb=" N BPHE E 244 " --> pdb=" O VAL E 240 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N ACYS E 245 " --> pdb=" O ALYS E 241 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N BGLY E 246 " --> pdb=" O BLEU E 242 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N BLEU E 247 " --> pdb=" O BGLY E 243 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N ILE E 248 " --> pdb=" O BPHE E 244 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N HIS E 249 " --> pdb=" O BCYS E 245 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 14 Processing sheet with id=AA2, first strand: chain 'A' and resid 271 through 273 removed outlier: 6.493A pdb=" N ILE A 271 " --> pdb=" O GLN A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 13 through 14 Processing sheet with id=AA4, first strand: chain 'B' and resid 271 through 273 removed outlier: 6.496A pdb=" N ILE B 271 " --> pdb=" O GLN B 278 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 13 through 14 Processing sheet with id=AA6, first strand: chain 'C' and resid 271 through 273 removed outlier: 6.493A pdb=" N ILE C 271 " --> pdb=" O GLN C 278 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 13 through 14 Processing sheet with id=AA8, first strand: chain 'D' and resid 271 through 273 removed outlier: 6.493A pdb=" N ILE D 271 " --> pdb=" O GLN D 278 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 13 through 14 Processing sheet with id=AB1, first strand: chain 'E' and resid 271 through 273 removed outlier: 6.495A pdb=" N ILE E 271 " --> pdb=" O GLN E 278 " (cutoff:3.500A) 975 hydrogen bonds defined for protein. 2840 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.74 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2896 1.33 - 1.46: 3533 1.46 - 1.59: 5200 1.59 - 1.72: 0 1.72 - 1.84: 85 Bond restraints: 11714 Sorted by residual: bond pdb=" C2 BRET A 402 " pdb=" C3 BRET A 402 " ideal model delta sigma weight residual 1.514 1.444 0.070 2.00e-02 2.50e+03 1.24e+01 bond pdb=" CA ALA A 97 " pdb=" CB ALA A 97 " ideal model delta sigma weight residual 1.533 1.485 0.048 1.39e-02 5.18e+03 1.20e+01 bond pdb=" CA SER B 67 " pdb=" CB SER B 67 " ideal model delta sigma weight residual 1.529 1.476 0.053 1.55e-02 4.16e+03 1.19e+01 bond pdb=" CA ALA E 97 " pdb=" CB ALA E 97 " ideal model delta sigma weight residual 1.533 1.486 0.047 1.39e-02 5.18e+03 1.16e+01 bond pdb=" CA ALA C 97 " pdb=" CB ALA C 97 " ideal model delta sigma weight residual 1.533 1.486 0.047 1.39e-02 5.18e+03 1.15e+01 ... (remaining 11709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 14781 2.53 - 5.06: 1136 5.06 - 7.59: 88 7.59 - 10.12: 15 10.12 - 12.66: 4 Bond angle restraints: 16024 Sorted by residual: angle pdb=" CA THR A 227 " pdb=" CB THR A 227 " pdb=" OG1 THR A 227 " ideal model delta sigma weight residual 109.60 101.76 7.84 1.50e+00 4.44e-01 2.73e+01 angle pdb=" CA ASP D 265 " pdb=" CB ASP D 265 " pdb=" CG ASP D 265 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.00e+00 1.00e+00 2.72e+01 angle pdb=" CA ASP A 265 " pdb=" CB ASP A 265 " pdb=" CG ASP A 265 " ideal model delta sigma weight residual 112.60 117.80 -5.20 1.00e+00 1.00e+00 2.70e+01 angle pdb=" CA ASP C 265 " pdb=" CB ASP C 265 " pdb=" CG ASP C 265 " ideal model delta sigma weight residual 112.60 117.79 -5.19 1.00e+00 1.00e+00 2.69e+01 angle pdb=" CA THR C 227 " pdb=" CB THR C 227 " pdb=" OG1 THR C 227 " ideal model delta sigma weight residual 109.60 101.82 7.78 1.50e+00 4.44e-01 2.69e+01 ... (remaining 16019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.16: 6687 24.16 - 48.33: 147 48.33 - 72.49: 36 72.49 - 96.66: 17 96.66 - 120.82: 7 Dihedral angle restraints: 6894 sinusoidal: 2649 harmonic: 4245 Sorted by residual: dihedral pdb=" CD ARG E 154 " pdb=" NE ARG E 154 " pdb=" CZ ARG E 154 " pdb=" NH1 ARG E 154 " ideal model delta sinusoidal sigma weight residual 0.00 62.15 -62.15 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CD ARG C 255 " pdb=" NE ARG C 255 " pdb=" CZ ARG C 255 " pdb=" NH1 ARG C 255 " ideal model delta sinusoidal sigma weight residual 0.00 -36.12 36.12 1 1.00e+01 1.00e-02 1.85e+01 dihedral pdb=" CD ARG B 255 " pdb=" NE ARG B 255 " pdb=" CZ ARG B 255 " pdb=" NH1 ARG B 255 " ideal model delta sinusoidal sigma weight residual 0.00 -35.77 35.77 1 1.00e+01 1.00e-02 1.81e+01 ... (remaining 6891 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1080 0.057 - 0.115: 649 0.115 - 0.172: 208 0.172 - 0.230: 38 0.230 - 0.287: 10 Chirality restraints: 1985 Sorted by residual: chirality pdb=" CA PHE B 24 " pdb=" N PHE B 24 " pdb=" C PHE B 24 " pdb=" CB PHE B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA PHE D 24 " pdb=" N PHE D 24 " pdb=" C PHE D 24 " pdb=" CB PHE D 24 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA PHE E 24 " pdb=" N PHE E 24 " pdb=" C PHE E 24 " pdb=" CB PHE E 24 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.06e+00 ... (remaining 1982 not shown) Planarity restraints: 1890 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 154 " 0.828 9.50e-02 1.11e+02 3.72e-01 9.31e+01 pdb=" NE ARG E 154 " -0.069 2.00e-02 2.50e+03 pdb=" CZ ARG E 154 " 0.043 2.00e-02 2.50e+03 pdb=" NH1 ARG E 154 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG E 154 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 38 " -0.572 9.50e-02 1.11e+02 2.57e-01 4.64e+01 pdb=" NE ARG A 38 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 38 " 0.050 2.00e-02 2.50e+03 pdb=" NH1 ARG A 38 " -0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 38 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 255 " -0.571 9.50e-02 1.11e+02 2.56e-01 4.17e+01 pdb=" NE ARG C 255 " 0.042 2.00e-02 2.50e+03 pdb=" CZ ARG C 255 " -0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG C 255 " 0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG C 255 " -0.011 2.00e-02 2.50e+03 ... (remaining 1887 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 1229 2.73 - 3.27: 12694 3.27 - 3.81: 23165 3.81 - 4.36: 28573 4.36 - 4.90: 46187 Nonbonded interactions: 111848 Sorted by model distance: nonbonded pdb=" NH2 ARG B 38 " pdb=" SG BCYS B 245 " model vdw 2.186 3.480 nonbonded pdb=" OD1 ASP E 152 " pdb=" O HOH E 501 " model vdw 2.211 3.040 nonbonded pdb=" NH2 ARG E 38 " pdb=" SG BCYS E 245 " model vdw 2.243 3.480 nonbonded pdb=" OD2 ASP D 80 " pdb=" O HOH D 501 " model vdw 2.263 3.040 nonbonded pdb=" OD2 ASP A 80 " pdb=" O HOH A 501 " model vdw 2.264 3.040 ... (remaining 111843 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 56 or resid 58 through 90 or (resid 91 through 9 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 93 through 1 \ 53 or (resid 154 and (name N or name CA or name C or name O or name CB or name C \ G or name CD or name NE )) or resid 155 through 200 or resid 206 through 240 or \ resid 248 through 285 or resid 401)) selection = (chain 'B' and (resid 3 through 56 or resid 58 through 90 or (resid 91 through 9 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 93 through 1 \ 28 or (resid 129 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 130 through 153 or (resid 154 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE )) or resid 155 through 178 o \ r (resid 179 through 180 and (name N or name CA or name C or name O or name CB ) \ ) or resid 181 or (resid 182 and (name N or name CA or name C or name O or name \ CB )) or resid 183 through 200 or resid 206 through 240 or resid 248 through 285 \ or resid 401)) selection = (chain 'C' and (resid 3 through 56 or resid 58 through 128 or (resid 129 and (na \ me N or name CA or name C or name O or name CB or name CG )) or resid 130 throug \ h 181 or (resid 182 and (name N or name CA or name C or name O or name CB )) or \ resid 183 through 200 or resid 206 through 240 or resid 248 through 285 or resid \ 401)) selection = (chain 'D' and (resid 3 through 56 or resid 58 through 90 or (resid 91 through 9 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 93 through 1 \ 28 or (resid 129 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 130 through 153 or (resid 154 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE )) or resid 155 through 200 o \ r resid 206 through 240 or resid 248 through 285 or resid 401)) selection = (chain 'E' and (resid 3 through 56 or resid 58 through 90 or (resid 91 through 9 \ 2 and (name N or name CA or name C or name O or name CB )) or resid 93 through 1 \ 28 or (resid 129 and (name N or name CA or name C or name O or name CB or name C \ G )) or resid 130 through 153 or (resid 154 and (name N or name CA or name C or \ name O or name CB or name CG or name CD or name NE )) or resid 155 through 200 o \ r resid 206 through 240 or resid 248 through 285 or resid 401)) } 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=0.50 max=1.00 mean=0.95 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: 21.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.630 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 39.030 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 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:16.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 77.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8765 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 : 0.013 0.078 11724 Z= 0.807 Angle : 1.462 12.656 16024 Z= 0.974 Chirality : 0.078 0.287 1985 Planarity : 0.022 0.372 1890 Dihedral : 13.728 120.820 4174 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.28 % Favored : 98.65 % Rotamer: Outliers : 0.97 % Allowed : 3.98 % Favored : 95.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.18), residues: 1500 helix: -0.58 (0.12), residues: 1120 sheet: None (None), residues: 0 loop : -1.02 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.013 TRP D 162 HIS 0.035 0.008 HIS D 81 PHE 0.050 0.013 PHE E 22 TYR 0.037 0.012 TYR E 210 ARG 0.052 0.009 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.17239 ( 975) hydrogen bonds : angle 7.11643 ( 2840) covalent geometry : bond 0.01269 (11714) covalent geometry : angle 1.46156 (16024) Misc. bond : bond 0.02422 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 133 time to evaluate : 1.332 Fit side-chains REVERT: B 182 ARG cc_start: 0.8485 (mtp180) cc_final: 0.7136 (mmt180) REVERT: C 187 GLN cc_start: 0.8592 (mt0) cc_final: 0.8289 (mt0) REVERT: D 187 GLN cc_start: 0.8588 (mt0) cc_final: 0.8335 (mt0) REVERT: E 187 GLN cc_start: 0.8493 (mt0) cc_final: 0.8259 (mt0) outliers start: 6 outliers final: 1 residues processed: 135 average time/residue: 1.6331 time to fit residues: 239.4352 Evaluate side-chains 117 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 116 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9990 chunk 106 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 127 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.098381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.080173 restraints weight = 89863.970| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.62 r_work: 0.2641 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11724 Z= 0.135 Angle : 0.604 9.671 16024 Z= 0.301 Chirality : 0.039 0.128 1985 Planarity : 0.005 0.063 1890 Dihedral : 9.784 98.521 1972 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 0.28 % Favored : 99.64 % Rotamer: Outliers : 0.88 % Allowed : 5.22 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.86 (0.21), residues: 1500 helix: 2.63 (0.14), residues: 1120 sheet: None (None), residues: 0 loop : -0.41 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP D 162 HIS 0.005 0.001 HIS D 18 PHE 0.014 0.002 PHE C 24 TYR 0.015 0.002 TYR B 68 ARG 0.010 0.001 ARG E 154 Details of bonding type rmsd hydrogen bonds : bond 0.04880 ( 975) hydrogen bonds : angle 4.05873 ( 2840) covalent geometry : bond 0.00266 (11714) covalent geometry : angle 0.60434 (16024) Misc. bond : bond 0.00016 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 1.118 Fit side-chains revert: symmetry clash REVERT: A 183 HIS cc_start: 0.8194 (t-90) cc_final: 0.7797 (t70) REVERT: B 66 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7787 (tp) REVERT: B 182 ARG cc_start: 0.8435 (mtp180) cc_final: 0.7036 (mmt180) REVERT: C 113 GLU cc_start: 0.8759 (tt0) cc_final: 0.8530 (tt0) REVERT: C 187 GLN cc_start: 0.8589 (mt0) cc_final: 0.8379 (mt0) REVERT: E 130 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7473 (tt) REVERT: E 187 GLN cc_start: 0.8536 (mt0) cc_final: 0.8200 (mt0) outliers start: 5 outliers final: 3 residues processed: 123 average time/residue: 1.3826 time to fit residues: 183.9172 Evaluate side-chains 119 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 114 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain E residue 130 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 40 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 133 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 35 optimal weight: 6.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.097134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.078762 restraints weight = 86111.405| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.55 r_work: 0.2635 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2522 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2522 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11724 Z= 0.159 Angle : 0.556 4.957 16024 Z= 0.295 Chirality : 0.041 0.135 1985 Planarity : 0.005 0.041 1890 Dihedral : 7.238 58.538 1972 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.14 % Favored : 98.79 % Rotamer: Outliers : 1.86 % Allowed : 5.84 % Favored : 92.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.22 (0.21), residues: 1500 helix: 2.89 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.25 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D 162 HIS 0.004 0.001 HIS D 81 PHE 0.019 0.003 PHE E 22 TYR 0.015 0.002 TYR C 68 ARG 0.004 0.001 ARG B 255 Details of bonding type rmsd hydrogen bonds : bond 0.05296 ( 975) hydrogen bonds : angle 3.96452 ( 2840) covalent geometry : bond 0.00343 (11714) covalent geometry : angle 0.55616 (16024) Misc. bond : bond 0.00035 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 HIS cc_start: 0.8185 (t-90) cc_final: 0.7772 (t-90) REVERT: B 66 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7788 (tp) REVERT: B 182 ARG cc_start: 0.8413 (mtp180) cc_final: 0.6984 (mmt180) REVERT: C 113 GLU cc_start: 0.8767 (tt0) cc_final: 0.8532 (tt0) REVERT: C 183 HIS cc_start: 0.8161 (t70) cc_final: 0.7757 (t70) REVERT: C 187 GLN cc_start: 0.8625 (mt0) cc_final: 0.8385 (mt0) REVERT: D 187 GLN cc_start: 0.8465 (mt0) cc_final: 0.8062 (mt0) REVERT: D 283 ILE cc_start: 0.7469 (OUTLIER) cc_final: 0.7256 (pt) REVERT: E 130 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7480 (tt) REVERT: E 187 GLN cc_start: 0.8584 (mt0) cc_final: 0.8255 (mt0) outliers start: 16 outliers final: 6 residues processed: 118 average time/residue: 1.4064 time to fit residues: 178.7804 Evaluate side-chains 123 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 114 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 14 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.097376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.078963 restraints weight = 86384.704| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.57 r_work: 0.2636 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2525 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2525 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2524 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2524 r_free = 0.2524 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2524 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11724 Z= 0.156 Angle : 0.547 4.930 16024 Z= 0.290 Chirality : 0.041 0.138 1985 Planarity : 0.005 0.036 1890 Dihedral : 7.248 58.878 1972 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 0.85 % Favored : 99.07 % Rotamer: Outliers : 2.21 % Allowed : 5.31 % Favored : 92.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.21), residues: 1500 helix: 2.91 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : -0.13 (0.32), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 162 HIS 0.004 0.001 HIS D 81 PHE 0.019 0.003 PHE E 22 TYR 0.015 0.002 TYR D 68 ARG 0.003 0.001 ARG A 255 Details of bonding type rmsd hydrogen bonds : bond 0.05190 ( 975) hydrogen bonds : angle 3.88995 ( 2840) covalent geometry : bond 0.00338 (11714) covalent geometry : angle 0.54677 (16024) Misc. bond : bond 0.00036 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.138 Fit side-chains REVERT: A 183 HIS cc_start: 0.8191 (t-90) cc_final: 0.7821 (t-90) REVERT: A 187 GLN cc_start: 0.8490 (mt0) cc_final: 0.8070 (mt0) REVERT: B 66 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.7798 (tp) REVERT: B 182 ARG cc_start: 0.8391 (mtp180) cc_final: 0.6960 (mmt180) REVERT: B 187 GLN cc_start: 0.8563 (mt0) cc_final: 0.8102 (mt0) REVERT: C 113 GLU cc_start: 0.8766 (tt0) cc_final: 0.8544 (tt0) REVERT: C 183 HIS cc_start: 0.8150 (t70) cc_final: 0.7793 (t70) REVERT: D 283 ILE cc_start: 0.7484 (OUTLIER) cc_final: 0.7272 (pt) REVERT: E 130 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7479 (tt) outliers start: 20 outliers final: 11 residues processed: 124 average time/residue: 1.3644 time to fit residues: 182.7115 Evaluate side-chains 128 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 114 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 119 optimal weight: 0.9990 chunk 67 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 135 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.097784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.079785 restraints weight = 83117.370| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 2.51 r_work: 0.2656 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2543 r_free = 0.2543 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11724 Z= 0.137 Angle : 0.518 4.923 16024 Z= 0.274 Chirality : 0.040 0.137 1985 Planarity : 0.005 0.036 1890 Dihedral : 7.017 59.367 1972 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.07 % Favored : 98.86 % Rotamer: Outliers : 2.04 % Allowed : 5.84 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.44 (0.21), residues: 1500 helix: 2.98 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : 0.06 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 162 HIS 0.004 0.001 HIS D 81 PHE 0.018 0.002 PHE B 22 TYR 0.014 0.002 TYR E 68 ARG 0.003 0.000 ARG E 255 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 975) hydrogen bonds : angle 3.77694 ( 2840) covalent geometry : bond 0.00287 (11714) covalent geometry : angle 0.51764 (16024) Misc. bond : bond 0.00022 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 187 GLN cc_start: 0.8476 (mt0) cc_final: 0.8031 (mt0) REVERT: B 66 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7800 (tp) REVERT: B 182 ARG cc_start: 0.8378 (mtp180) cc_final: 0.6954 (mmt180) REVERT: B 187 GLN cc_start: 0.8541 (mt0) cc_final: 0.8142 (mt0) REVERT: C 113 GLU cc_start: 0.8757 (tt0) cc_final: 0.8534 (tt0) REVERT: C 183 HIS cc_start: 0.8128 (t70) cc_final: 0.7791 (t70) REVERT: D 187 GLN cc_start: 0.8471 (mt0) cc_final: 0.8029 (mt0) REVERT: D 283 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7297 (pt) REVERT: E 130 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7478 (tt) outliers start: 18 outliers final: 12 residues processed: 125 average time/residue: 1.3426 time to fit residues: 181.7433 Evaluate side-chains 130 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 133 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 126 optimal weight: 0.0000 chunk 18 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 overall best weight: 1.3390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.097699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.079616 restraints weight = 87225.996| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.56 r_work: 0.2647 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2534 r_free = 0.2534 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11724 Z= 0.144 Angle : 0.528 4.932 16024 Z= 0.279 Chirality : 0.040 0.138 1985 Planarity : 0.005 0.036 1890 Dihedral : 7.028 59.462 1972 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.14 % Favored : 98.79 % Rotamer: Outliers : 2.30 % Allowed : 5.66 % Favored : 92.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.21), residues: 1500 helix: 2.96 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : 0.07 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 162 HIS 0.004 0.001 HIS D 81 PHE 0.018 0.002 PHE B 22 TYR 0.014 0.002 TYR D 68 ARG 0.002 0.000 ARG E 255 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 975) hydrogen bonds : angle 3.76867 ( 2840) covalent geometry : bond 0.00308 (11714) covalent geometry : angle 0.52772 (16024) Misc. bond : bond 0.00032 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.156 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.8474 (mt0) cc_final: 0.8022 (mt0) REVERT: B 66 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7801 (tp) REVERT: B 182 ARG cc_start: 0.8383 (mtp180) cc_final: 0.6953 (mmt180) REVERT: C 113 GLU cc_start: 0.8762 (tt0) cc_final: 0.8502 (tt0) REVERT: C 183 HIS cc_start: 0.8138 (t70) cc_final: 0.7797 (t70) REVERT: D 187 GLN cc_start: 0.8462 (mt0) cc_final: 0.8041 (mt0) REVERT: D 283 ILE cc_start: 0.7495 (OUTLIER) cc_final: 0.7279 (pt) REVERT: E 130 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7487 (tt) outliers start: 21 outliers final: 16 residues processed: 126 average time/residue: 1.3236 time to fit residues: 180.9246 Evaluate side-chains 133 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 132 optimal weight: 0.0000 chunk 136 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 128 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 113 optimal weight: 4.9990 overall best weight: 0.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.099359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.081003 restraints weight = 83348.994| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.54 r_work: 0.2675 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2562 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.11 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2562 r_free = 0.2562 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2562 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11724 Z= 0.124 Angle : 0.498 5.376 16024 Z= 0.263 Chirality : 0.039 0.136 1985 Planarity : 0.004 0.035 1890 Dihedral : 6.757 58.999 1972 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.35 % Favored : 98.58 % Rotamer: Outliers : 2.12 % Allowed : 5.75 % Favored : 92.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.21), residues: 1500 helix: 3.09 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : 0.18 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 162 HIS 0.004 0.001 HIS E 18 PHE 0.015 0.002 PHE B 22 TYR 0.013 0.002 TYR B 68 ARG 0.002 0.000 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.04554 ( 975) hydrogen bonds : angle 3.63970 ( 2840) covalent geometry : bond 0.00250 (11714) covalent geometry : angle 0.49849 (16024) Misc. bond : bond 0.00010 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 1.422 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 183 HIS cc_start: 0.8143 (t70) cc_final: 0.7906 (t-90) REVERT: A 187 GLN cc_start: 0.8459 (mt0) cc_final: 0.8000 (mt0) REVERT: B 62 ILE cc_start: 0.8736 (mt) cc_final: 0.8331 (pp) REVERT: B 66 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.7790 (tp) REVERT: B 182 ARG cc_start: 0.8371 (mtp180) cc_final: 0.6925 (mmt180) REVERT: B 187 GLN cc_start: 0.8547 (mt0) cc_final: 0.8107 (mt0) REVERT: C 113 GLU cc_start: 0.8748 (tt0) cc_final: 0.8508 (tt0) REVERT: C 183 HIS cc_start: 0.8113 (t70) cc_final: 0.7776 (t70) REVERT: D 187 GLN cc_start: 0.8445 (mt0) cc_final: 0.8018 (mt0) REVERT: E 130 LEU cc_start: 0.8166 (OUTLIER) cc_final: 0.7479 (tt) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 1.5490 time to fit residues: 210.5636 Evaluate side-chains 131 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 1.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 37 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.097688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.079633 restraints weight = 85346.932| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.54 r_work: 0.2650 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2538 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.2538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2530 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2530 r_free = 0.2530 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2530 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11724 Z= 0.146 Angle : 0.530 5.816 16024 Z= 0.279 Chirality : 0.040 0.138 1985 Planarity : 0.005 0.036 1890 Dihedral : 6.981 59.522 1972 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.00 % Favored : 98.93 % Rotamer: Outliers : 2.21 % Allowed : 5.84 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.49 (0.21), residues: 1500 helix: 2.99 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : 0.17 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 162 HIS 0.004 0.001 HIS D 81 PHE 0.019 0.002 PHE E 22 TYR 0.014 0.002 TYR C 68 ARG 0.002 0.001 ARG E 51 Details of bonding type rmsd hydrogen bonds : bond 0.04960 ( 975) hydrogen bonds : angle 3.71582 ( 2840) covalent geometry : bond 0.00314 (11714) covalent geometry : angle 0.52999 (16024) Misc. bond : bond 0.00035 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 114 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.8465 (mt0) cc_final: 0.8020 (mt0) REVERT: B 66 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7796 (tp) REVERT: B 182 ARG cc_start: 0.8379 (mtp180) cc_final: 0.6940 (mmt180) REVERT: B 187 GLN cc_start: 0.8571 (mt0) cc_final: 0.8177 (mt0) REVERT: C 113 GLU cc_start: 0.8765 (tt0) cc_final: 0.8525 (tt0) REVERT: C 183 HIS cc_start: 0.8127 (t70) cc_final: 0.7792 (t70) REVERT: D 187 GLN cc_start: 0.8444 (mt0) cc_final: 0.7998 (mt0) REVERT: E 130 LEU cc_start: 0.8165 (OUTLIER) cc_final: 0.7471 (tt) outliers start: 20 outliers final: 16 residues processed: 126 average time/residue: 1.5865 time to fit residues: 216.1707 Evaluate side-chains 131 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 50 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 chunk 105 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.097768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.079446 restraints weight = 80346.246| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.51 r_work: 0.2645 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2535 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2535 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2535 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2535 r_free = 0.2535 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2535 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11724 Z= 0.153 Angle : 0.541 5.977 16024 Z= 0.285 Chirality : 0.041 0.139 1985 Planarity : 0.005 0.040 1890 Dihedral : 7.150 59.866 1972 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.07 % Favored : 98.86 % Rotamer: Outliers : 2.12 % Allowed : 5.93 % Favored : 91.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.45 (0.21), residues: 1500 helix: 2.98 (0.15), residues: 1115 sheet: None (None), residues: 0 loop : 0.11 (0.33), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 162 HIS 0.004 0.001 HIS D 81 PHE 0.019 0.003 PHE E 22 TYR 0.014 0.002 TYR B 68 ARG 0.002 0.001 ARG E 99 Details of bonding type rmsd hydrogen bonds : bond 0.05064 ( 975) hydrogen bonds : angle 3.74156 ( 2840) covalent geometry : bond 0.00334 (11714) covalent geometry : angle 0.54055 (16024) Misc. bond : bond 0.00043 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 1.081 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.8466 (mt0) cc_final: 0.8008 (mt0) REVERT: B 66 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7809 (tp) REVERT: B 182 ARG cc_start: 0.8364 (mtp180) cc_final: 0.6947 (mmt180) REVERT: B 187 GLN cc_start: 0.8576 (mt0) cc_final: 0.8179 (mt0) REVERT: C 113 GLU cc_start: 0.8757 (tt0) cc_final: 0.8496 (tt0) REVERT: C 183 HIS cc_start: 0.8134 (t70) cc_final: 0.7801 (t70) REVERT: D 187 GLN cc_start: 0.8448 (mt0) cc_final: 0.7993 (mt0) REVERT: E 130 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7479 (tt) outliers start: 19 outliers final: 16 residues processed: 125 average time/residue: 1.8386 time to fit residues: 248.9163 Evaluate side-chains 130 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 112 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 108 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 41 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 131 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 127 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 110 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.099016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.080760 restraints weight = 77630.903| |-----------------------------------------------------------------------------| r_work (start): 0.2821 rms_B_bonded: 2.48 r_work: 0.2673 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2560 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2560 r_free = 0.2560 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11724 Z= 0.128 Angle : 0.510 6.979 16024 Z= 0.268 Chirality : 0.039 0.137 1985 Planarity : 0.004 0.040 1890 Dihedral : 6.957 59.977 1972 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.35 % Favored : 98.58 % Rotamer: Outliers : 2.04 % Allowed : 6.11 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.21), residues: 1500 helix: 3.07 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : 0.26 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 162 HIS 0.004 0.001 HIS E 18 PHE 0.017 0.002 PHE E 22 TYR 0.013 0.002 TYR B 68 ARG 0.004 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.04616 ( 975) hydrogen bonds : angle 3.63260 ( 2840) covalent geometry : bond 0.00264 (11714) covalent geometry : angle 0.51002 (16024) Misc. bond : bond 0.00015 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3000 Ramachandran restraints generated. 1500 Oldfield, 0 Emsley, 1500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.8457 (mt0) cc_final: 0.8014 (mt0) REVERT: B 62 ILE cc_start: 0.8718 (mt) cc_final: 0.8341 (pp) REVERT: B 66 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.7778 (tp) REVERT: B 182 ARG cc_start: 0.8372 (mtp180) cc_final: 0.6927 (mmt180) REVERT: B 187 GLN cc_start: 0.8564 (mt0) cc_final: 0.8158 (mt0) REVERT: C 113 GLU cc_start: 0.8752 (tt0) cc_final: 0.8528 (tt0) REVERT: C 183 HIS cc_start: 0.8114 (t70) cc_final: 0.7777 (t70) REVERT: E 130 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7491 (tt) outliers start: 18 outliers final: 16 residues processed: 125 average time/residue: 1.5832 time to fit residues: 215.0322 Evaluate side-chains 131 residues out of total 1065 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 113 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 124 SER Chi-restraints excluded: chain A residue 224 LEU Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 124 SER Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain C residue 124 SER Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain D residue 124 SER Chi-restraints excluded: chain D residue 224 LEU Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain E residue 124 SER Chi-restraints excluded: chain E residue 130 LEU Chi-restraints excluded: chain E residue 224 LEU Chi-restraints excluded: chain E residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 9 optimal weight: 0.6980 chunk 104 optimal weight: 0.0770 chunk 122 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 43 optimal weight: 0.0980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.101524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.083456 restraints weight = 87314.145| |-----------------------------------------------------------------------------| r_work (start): 0.2862 rms_B_bonded: 2.56 r_work: 0.2713 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 11724 Z= 0.109 Angle : 0.480 7.210 16024 Z= 0.251 Chirality : 0.038 0.135 1985 Planarity : 0.004 0.035 1890 Dihedral : 6.539 58.857 1972 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.28 % Favored : 98.65 % Rotamer: Outliers : 1.77 % Allowed : 6.37 % Favored : 91.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.88 (0.22), residues: 1500 helix: 3.27 (0.15), residues: 1120 sheet: None (None), residues: 0 loop : 0.30 (0.34), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 162 HIS 0.004 0.001 HIS C 18 PHE 0.014 0.002 PHE E 22 TYR 0.012 0.002 TYR A 68 ARG 0.002 0.000 ARG D 38 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 975) hydrogen bonds : angle 3.49721 ( 2840) covalent geometry : bond 0.00209 (11714) covalent geometry : angle 0.47969 (16024) Misc. bond : bond 0.00011 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11025.60 seconds wall clock time: 198 minutes 25.11 seconds (11905.11 seconds total)