Starting phenix.real_space_refine on Sun Feb 18 18:00:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teh_10490/02_2024/6teh_10490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teh_10490/02_2024/6teh_10490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.99 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teh_10490/02_2024/6teh_10490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teh_10490/02_2024/6teh_10490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teh_10490/02_2024/6teh_10490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6teh_10490/02_2024/6teh_10490_updated.pdb" } resolution = 3.99 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= 0.001 sd= 0.005 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: 5 Type Number sf(0) Gaussians Fe 12 7.16 5 S 54 5.16 5 C 14181 2.51 5 N 4143 2.21 5 O 4245 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 26": "NH1" <-> "NH2" Residue "C PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 114": "NH1" <-> "NH2" Residue "C ARG 122": "NH1" <-> "NH2" Residue "C ARG 149": "NH1" <-> "NH2" Residue "C PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 200": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 62": "NH1" <-> "NH2" Residue "D ARG 74": "NH1" <-> "NH2" Residue "D ARG 78": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 128": "NH1" <-> "NH2" Residue "D ARG 131": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 214": "OD1" <-> "OD2" Residue "D ARG 220": "NH1" <-> "NH2" Residue "D ARG 760": "NH1" <-> "NH2" Residue "D ASP 783": "OD1" <-> "OD2" Residue "D PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 848": "OE1" <-> "OE2" Residue "D ARG 855": "NH1" <-> "NH2" Residue "D PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 913": "NH1" <-> "NH2" Residue "D PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 933": "NH1" <-> "NH2" Residue "D ARG 951": "NH1" <-> "NH2" Residue "D ARG 970": "NH1" <-> "NH2" Residue "B GLU 21": "OE1" <-> "OE2" Residue "B ARG 44": "NH1" <-> "NH2" Residue "B ARG 69": "NH1" <-> "NH2" Residue "B ARG 170": "NH1" <-> "NH2" Residue "B PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 44": "NH1" <-> "NH2" Residue "A ARG 69": "NH1" <-> "NH2" Residue "A ARG 170": "NH1" <-> "NH2" Residue "A PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 26": "NH1" <-> "NH2" Residue "E PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 114": "NH1" <-> "NH2" Residue "E ARG 122": "NH1" <-> "NH2" Residue "E ARG 149": "NH1" <-> "NH2" Residue "E PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 200": "NH1" <-> "NH2" Residue "E ARG 243": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 62": "NH1" <-> "NH2" Residue "F ARG 74": "NH1" <-> "NH2" Residue "F ARG 78": "NH1" <-> "NH2" Residue "F ARG 90": "NH1" <-> "NH2" Residue "F ARG 128": "NH1" <-> "NH2" Residue "F ARG 131": "NH1" <-> "NH2" Residue "F ARG 147": "NH1" <-> "NH2" Residue "F PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 214": "OD1" <-> "OD2" Residue "F ARG 220": "NH1" <-> "NH2" Residue "F ARG 760": "NH1" <-> "NH2" Residue "F ASP 783": "OD1" <-> "OD2" Residue "F PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 848": "OE1" <-> "OE2" Residue "F ARG 855": "NH1" <-> "NH2" Residue "F PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 913": "NH1" <-> "NH2" Residue "F PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 933": "NH1" <-> "NH2" Residue "F ARG 951": "NH1" <-> "NH2" Residue "F ARG 970": "NH1" <-> "NH2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G ARG 44": "NH1" <-> "NH2" Residue "G ARG 69": "NH1" <-> "NH2" Residue "G ARG 170": "NH1" <-> "NH2" Residue "G PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 44": "NH1" <-> "NH2" Residue "H ARG 69": "NH1" <-> "NH2" Residue "H ARG 170": "NH1" <-> "NH2" Residue "H PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 26": "NH1" <-> "NH2" Residue "I PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 114": "NH1" <-> "NH2" Residue "I ARG 122": "NH1" <-> "NH2" Residue "I ARG 149": "NH1" <-> "NH2" Residue "I PHE 191": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 200": "NH1" <-> "NH2" Residue "I ARG 243": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 62": "NH1" <-> "NH2" Residue "J ARG 74": "NH1" <-> "NH2" Residue "J ARG 78": "NH1" <-> "NH2" Residue "J ARG 90": "NH1" <-> "NH2" Residue "J ARG 128": "NH1" <-> "NH2" Residue "J ARG 131": "NH1" <-> "NH2" Residue "J ARG 147": "NH1" <-> "NH2" Residue "J PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 198": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ASP 214": "OD1" <-> "OD2" Residue "J ARG 220": "NH1" <-> "NH2" Residue "J ARG 760": "NH1" <-> "NH2" Residue "J ASP 783": "OD1" <-> "OD2" Residue "J PHE 815": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 848": "OE1" <-> "OE2" Residue "J ARG 855": "NH1" <-> "NH2" Residue "J PHE 876": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 913": "NH1" <-> "NH2" Residue "J PHE 927": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 933": "NH1" <-> "NH2" Residue "J ARG 951": "NH1" <-> "NH2" Residue "J ARG 970": "NH1" <-> "NH2" Residue "K GLU 21": "OE1" <-> "OE2" Residue "K ARG 44": "NH1" <-> "NH2" Residue "K ARG 69": "NH1" <-> "NH2" Residue "K ARG 170": "NH1" <-> "NH2" Residue "K PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 44": "NH1" <-> "NH2" Residue "L ARG 69": "NH1" <-> "NH2" Residue "L ARG 170": "NH1" <-> "NH2" Residue "L PHE 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 22635 Number of models: 1 Model: "" Number of chains: 15 Chain: "C" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2179 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "D" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3246 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2179 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "F" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3246 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "H" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 2179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2179 Classifications: {'peptide': 292} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 8, 'TRANS': 283} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "J" Number of atoms: 3246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3246 Classifications: {'peptide': 439} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'CIS': 1, 'PTRANS': 14, 'TRANS': 423} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "L" Number of atoms: 1056 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1056 Classifications: {'peptide': 134} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1827 SG CYS C 250 33.585 31.455 90.674 1.00 69.30 S ATOM 9372 SG CYS E 250 100.428 42.631 90.674 1.00 69.30 S ATOM 16917 SG CYS I 250 57.327 94.931 90.674 1.00 69.30 S Time building chain proxies: 13.23, per 1000 atoms: 0.58 Number of scatterers: 22635 At special positions: 0 Unit cell: (122.245, 125.434, 138.19, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 12 26.01 S 54 16.00 O 4245 8.00 N 4143 7.00 C 14181 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.29 Conformation dependent library (CDL) restraints added in 4.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 301 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 250 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 150 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 159 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 257 " pdb=" SF4 E 301 " pdb="FE2 SF4 E 301 " - pdb=" SG CYS E 250 " pdb="FE4 SF4 E 301 " - pdb=" SG CYS E 150 " pdb="FE3 SF4 E 301 " - pdb=" SG CYS E 159 " pdb="FE1 SF4 E 301 " - pdb=" SG CYS E 257 " pdb=" SF4 I 301 " pdb="FE2 SF4 I 301 " - pdb=" SG CYS I 250 " pdb="FE4 SF4 I 301 " - pdb=" SG CYS I 150 " pdb="FE3 SF4 I 301 " - pdb=" SG CYS I 159 " pdb="FE1 SF4 I 301 " - pdb=" SG CYS I 257 " Number of angles added : 36 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5262 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 57 helices and 30 sheets defined 12.1% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.16 Creating SS restraints... Processing helix chain 'C' and resid 8 through 12 Processing helix chain 'C' and resid 84 through 88 removed outlier: 3.699A pdb=" N ALA C 88 " --> pdb=" O ALA C 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 84 through 88' Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 254 through 260 Processing helix chain 'C' and resid 276 through 279 No H-bonds generated for 'chain 'C' and resid 276 through 279' Processing helix chain 'D' and resid 10 through 13 No H-bonds generated for 'chain 'D' and resid 10 through 13' Processing helix chain 'D' and resid 18 through 22 removed outlier: 3.729A pdb=" N LEU D 22 " --> pdb=" O GLY D 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 18 through 22' Processing helix chain 'D' and resid 42 through 46 removed outlier: 3.580A pdb=" N LEU D 46 " --> pdb=" O ASP D 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 42 through 46' Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 167 through 169 No H-bonds generated for 'chain 'D' and resid 167 through 169' Processing helix chain 'D' and resid 207 through 210 No H-bonds generated for 'chain 'D' and resid 207 through 210' Processing helix chain 'D' and resid 215 through 218 No H-bonds generated for 'chain 'D' and resid 215 through 218' Processing helix chain 'D' and resid 766 through 777 Processing helix chain 'D' and resid 803 through 812 removed outlier: 3.732A pdb=" N ALA D 808 " --> pdb=" O ALA D 804 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU D 809 " --> pdb=" O GLY D 805 " (cutoff:3.500A) Processing helix chain 'D' and resid 839 through 841 No H-bonds generated for 'chain 'D' and resid 839 through 841' Processing helix chain 'D' and resid 904 through 922 removed outlier: 3.515A pdb=" N GLN D 908 " --> pdb=" O ARG D 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA D 916 " --> pdb=" O GLY D 912 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG D 919 " --> pdb=" O LEU D 915 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG D 922 " --> pdb=" O ALA D 918 " (cutoff:3.500A) Processing helix chain 'D' and resid 931 through 933 No H-bonds generated for 'chain 'D' and resid 931 through 933' Processing helix chain 'B' and resid 57 through 67 removed outlier: 4.326A pdb=" N ARG B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 64 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 67 removed outlier: 4.330A pdb=" N ARG A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE A 66 " --> pdb=" O LEU A 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 8 through 12 Processing helix chain 'E' and resid 84 through 88 removed outlier: 3.699A pdb=" N ALA E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 84 through 88' Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 254 through 260 Processing helix chain 'E' and resid 276 through 279 No H-bonds generated for 'chain 'E' and resid 276 through 279' Processing helix chain 'F' and resid 10 through 13 No H-bonds generated for 'chain 'F' and resid 10 through 13' Processing helix chain 'F' and resid 18 through 22 removed outlier: 3.730A pdb=" N LEU F 22 " --> pdb=" O GLY F 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 18 through 22' Processing helix chain 'F' and resid 42 through 46 removed outlier: 3.579A pdb=" N LEU F 46 " --> pdb=" O ASP F 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 42 through 46' Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 167 through 169 No H-bonds generated for 'chain 'F' and resid 167 through 169' Processing helix chain 'F' and resid 207 through 210 No H-bonds generated for 'chain 'F' and resid 207 through 210' Processing helix chain 'F' and resid 215 through 218 No H-bonds generated for 'chain 'F' and resid 215 through 218' Processing helix chain 'F' and resid 766 through 777 Processing helix chain 'F' and resid 803 through 812 removed outlier: 3.732A pdb=" N ALA F 808 " --> pdb=" O ALA F 804 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU F 809 " --> pdb=" O GLY F 805 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 841 No H-bonds generated for 'chain 'F' and resid 839 through 841' Processing helix chain 'F' and resid 904 through 922 removed outlier: 3.515A pdb=" N GLN F 908 " --> pdb=" O ARG F 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA F 916 " --> pdb=" O GLY F 912 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG F 919 " --> pdb=" O LEU F 915 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG F 922 " --> pdb=" O ALA F 918 " (cutoff:3.500A) Processing helix chain 'F' and resid 931 through 933 No H-bonds generated for 'chain 'F' and resid 931 through 933' Processing helix chain 'G' and resid 57 through 67 removed outlier: 4.326A pdb=" N ARG G 61 " --> pdb=" O ASP G 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE G 65 " --> pdb=" O ARG G 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 67 removed outlier: 4.330A pdb=" N ARG H 61 " --> pdb=" O ASP H 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE H 65 " --> pdb=" O ARG H 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE H 66 " --> pdb=" O LEU H 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 8 through 12 Processing helix chain 'I' and resid 84 through 88 removed outlier: 3.699A pdb=" N ALA I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 84 through 88' Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 254 through 260 Processing helix chain 'I' and resid 276 through 279 No H-bonds generated for 'chain 'I' and resid 276 through 279' Processing helix chain 'J' and resid 10 through 13 No H-bonds generated for 'chain 'J' and resid 10 through 13' Processing helix chain 'J' and resid 18 through 22 removed outlier: 3.730A pdb=" N LEU J 22 " --> pdb=" O GLY J 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 18 through 22' Processing helix chain 'J' and resid 42 through 46 removed outlier: 3.580A pdb=" N LEU J 46 " --> pdb=" O ASP J 42 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 42 through 46' Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 167 through 169 No H-bonds generated for 'chain 'J' and resid 167 through 169' Processing helix chain 'J' and resid 207 through 210 No H-bonds generated for 'chain 'J' and resid 207 through 210' Processing helix chain 'J' and resid 215 through 218 No H-bonds generated for 'chain 'J' and resid 215 through 218' Processing helix chain 'J' and resid 766 through 777 Processing helix chain 'J' and resid 803 through 812 removed outlier: 3.732A pdb=" N ALA J 808 " --> pdb=" O ALA J 804 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LEU J 809 " --> pdb=" O GLY J 805 " (cutoff:3.500A) Processing helix chain 'J' and resid 839 through 841 No H-bonds generated for 'chain 'J' and resid 839 through 841' Processing helix chain 'J' and resid 904 through 922 removed outlier: 3.515A pdb=" N GLN J 908 " --> pdb=" O ARG J 904 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA J 916 " --> pdb=" O GLY J 912 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG J 919 " --> pdb=" O LEU J 915 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ARG J 922 " --> pdb=" O ALA J 918 " (cutoff:3.500A) Processing helix chain 'J' and resid 931 through 933 No H-bonds generated for 'chain 'J' and resid 931 through 933' Processing helix chain 'K' and resid 57 through 67 removed outlier: 4.326A pdb=" N ARG K 61 " --> pdb=" O ASP K 57 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA K 64 " --> pdb=" O GLU K 60 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE K 65 " --> pdb=" O ARG K 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 67 removed outlier: 4.330A pdb=" N ARG L 61 " --> pdb=" O ASP L 57 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA L 64 " --> pdb=" O GLU L 60 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N PHE L 65 " --> pdb=" O ARG L 61 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N PHE L 66 " --> pdb=" O LEU L 62 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 95 through 102 Processing sheet with id= B, first strand: chain 'C' and resid 119 through 123 Processing sheet with id= C, first strand: chain 'C' and resid 211 through 214 Processing sheet with id= D, first strand: chain 'D' and resid 74 through 76 Processing sheet with id= E, first strand: chain 'D' and resid 79 through 81 Processing sheet with id= F, first strand: chain 'D' and resid 851 through 854 removed outlier: 3.622A pdb=" N ALA D 925 " --> pdb=" O ALA D 968 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 882 through 884 Processing sheet with id= H, first strand: chain 'D' and resid 118 through 123 removed outlier: 6.551A pdb=" N ALA D 177 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 52 through 54 removed outlier: 3.942A pdb=" N GLY B 52 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU B 200 " --> pdb=" O GLY B 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG B 54 " --> pdb=" O GLY B 198 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER B 194 " --> pdb=" O ALA B 197 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP B 199 " --> pdb=" O VAL B 192 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL B 192 " --> pdb=" O ASP B 199 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'A' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY A 52 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU A 200 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG A 54 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER A 194 " --> pdb=" O ALA A 197 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP A 199 " --> pdb=" O VAL A 192 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL A 192 " --> pdb=" O ASP A 199 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'E' and resid 95 through 102 Processing sheet with id= L, first strand: chain 'E' and resid 119 through 123 Processing sheet with id= M, first strand: chain 'E' and resid 211 through 214 Processing sheet with id= N, first strand: chain 'F' and resid 74 through 76 Processing sheet with id= O, first strand: chain 'F' and resid 79 through 81 Processing sheet with id= P, first strand: chain 'F' and resid 851 through 854 removed outlier: 3.622A pdb=" N ALA F 925 " --> pdb=" O ALA F 968 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 882 through 884 Processing sheet with id= R, first strand: chain 'F' and resid 118 through 123 removed outlier: 6.550A pdb=" N ALA F 177 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 52 through 54 removed outlier: 3.942A pdb=" N GLY G 52 " --> pdb=" O LEU G 200 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU G 200 " --> pdb=" O GLY G 52 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG G 54 " --> pdb=" O GLY G 198 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER G 194 " --> pdb=" O ALA G 197 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP G 199 " --> pdb=" O VAL G 192 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL G 192 " --> pdb=" O ASP G 199 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'H' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY H 52 " --> pdb=" O LEU H 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU H 200 " --> pdb=" O GLY H 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG H 54 " --> pdb=" O GLY H 198 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER H 194 " --> pdb=" O ALA H 197 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP H 199 " --> pdb=" O VAL H 192 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N VAL H 192 " --> pdb=" O ASP H 199 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 95 through 102 Processing sheet with id= V, first strand: chain 'I' and resid 119 through 123 Processing sheet with id= W, first strand: chain 'I' and resid 211 through 214 Processing sheet with id= X, first strand: chain 'J' and resid 74 through 76 Processing sheet with id= Y, first strand: chain 'J' and resid 79 through 81 Processing sheet with id= Z, first strand: chain 'J' and resid 851 through 854 removed outlier: 3.622A pdb=" N ALA J 925 " --> pdb=" O ALA J 968 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'J' and resid 882 through 884 Processing sheet with id= AB, first strand: chain 'J' and resid 118 through 123 removed outlier: 6.550A pdb=" N ALA J 177 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'K' and resid 52 through 54 removed outlier: 3.943A pdb=" N GLY K 52 " --> pdb=" O LEU K 200 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU K 200 " --> pdb=" O GLY K 52 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG K 54 " --> pdb=" O GLY K 198 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER K 194 " --> pdb=" O ALA K 197 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ASP K 199 " --> pdb=" O VAL K 192 " (cutoff:3.500A) removed outlier: 5.196A pdb=" N VAL K 192 " --> pdb=" O ASP K 199 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 52 through 54 removed outlier: 3.944A pdb=" N GLY L 52 " --> pdb=" O LEU L 200 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N LEU L 200 " --> pdb=" O GLY L 52 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG L 54 " --> pdb=" O GLY L 198 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER L 194 " --> pdb=" O ALA L 197 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ASP L 199 " --> pdb=" O VAL L 192 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N VAL L 192 " --> pdb=" O ASP L 199 " (cutoff:3.500A) 270 hydrogen bonds defined for protein. 693 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: 5.93 Time building geometry restraints manager: 10.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 10006 1.43 - 1.64: 12980 1.64 - 1.85: 66 1.85 - 2.06: 0 2.06 - 2.27: 36 Bond restraints: 23088 Sorted by residual: bond pdb=" N ILE F 782 " pdb=" CA ILE F 782 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.27e-02 6.20e+03 1.12e+01 bond pdb=" N ILE J 782 " pdb=" CA ILE J 782 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.27e-02 6.20e+03 1.11e+01 bond pdb=" N ILE D 782 " pdb=" CA ILE D 782 " ideal model delta sigma weight residual 1.458 1.499 -0.042 1.27e-02 6.20e+03 1.08e+01 bond pdb=" C ILE F 225 " pdb=" N PRO F 226 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.36e-02 5.41e+03 1.00e+01 bond pdb=" C ILE D 225 " pdb=" N PRO D 226 " ideal model delta sigma weight residual 1.335 1.378 -0.043 1.36e-02 5.41e+03 9.90e+00 ... (remaining 23083 not shown) Histogram of bond angle deviations from ideal: 73.50 - 85.65: 36 85.65 - 97.80: 0 97.80 - 109.95: 4217 109.95 - 122.10: 22132 122.10 - 134.24: 4926 Bond angle restraints: 31311 Sorted by residual: angle pdb=" C ILE D 225 " pdb=" N PRO D 226 " pdb=" CA PRO D 226 " ideal model delta sigma weight residual 119.05 125.47 -6.42 1.11e+00 8.12e-01 3.35e+01 angle pdb=" C ILE F 225 " pdb=" N PRO F 226 " pdb=" CA PRO F 226 " ideal model delta sigma weight residual 119.05 125.45 -6.40 1.11e+00 8.12e-01 3.33e+01 angle pdb=" C ILE J 225 " pdb=" N PRO J 226 " pdb=" CA PRO J 226 " ideal model delta sigma weight residual 119.05 125.45 -6.40 1.11e+00 8.12e-01 3.32e+01 angle pdb=" C PRO D 159 " pdb=" N LYS D 160 " pdb=" CA LYS D 160 " ideal model delta sigma weight residual 121.54 131.40 -9.86 1.91e+00 2.74e-01 2.67e+01 angle pdb=" C PRO F 159 " pdb=" N LYS F 160 " pdb=" CA LYS F 160 " ideal model delta sigma weight residual 121.54 131.38 -9.84 1.91e+00 2.74e-01 2.65e+01 ... (remaining 31306 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.52: 11984 14.52 - 29.03: 1183 29.03 - 43.54: 297 43.54 - 58.06: 21 58.06 - 72.57: 15 Dihedral angle restraints: 13500 sinusoidal: 5214 harmonic: 8286 Sorted by residual: dihedral pdb=" CA LEU F 215 " pdb=" C LEU F 215 " pdb=" N THR F 216 " pdb=" CA THR F 216 " ideal model delta harmonic sigma weight residual -180.00 -150.04 -29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU J 215 " pdb=" C LEU J 215 " pdb=" N THR J 216 " pdb=" CA THR J 216 " ideal model delta harmonic sigma weight residual -180.00 -150.04 -29.96 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA LEU D 215 " pdb=" C LEU D 215 " pdb=" N THR D 216 " pdb=" CA THR D 216 " ideal model delta harmonic sigma weight residual -180.00 -150.07 -29.93 0 5.00e+00 4.00e-02 3.58e+01 ... (remaining 13497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2358 0.063 - 0.127: 802 0.127 - 0.190: 190 0.190 - 0.253: 52 0.253 - 0.316: 6 Chirality restraints: 3408 Sorted by residual: chirality pdb=" CB ILE C 273 " pdb=" CA ILE C 273 " pdb=" CG1 ILE C 273 " pdb=" CG2 ILE C 273 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CB ILE E 273 " pdb=" CA ILE E 273 " pdb=" CG1 ILE E 273 " pdb=" CG2 ILE E 273 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CB ILE I 273 " pdb=" CA ILE I 273 " pdb=" CG1 ILE I 273 " pdb=" CG2 ILE I 273 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.48e+00 ... (remaining 3405 not shown) Planarity restraints: 4188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO K 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO K 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO K 166 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO B 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO B 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 166 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO G 165 " 0.054 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO G 166 " -0.143 5.00e-02 4.00e+02 pdb=" CA PRO G 166 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO G 166 " 0.046 5.00e-02 4.00e+02 ... (remaining 4185 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4748 2.77 - 3.30: 21861 3.30 - 3.84: 37542 3.84 - 4.37: 43003 4.37 - 4.90: 72157 Nonbonded interactions: 179311 Sorted by model distance: nonbonded pdb=" O LEU E 18 " pdb=" ND2 ASN H 37 " model vdw 2.239 2.520 nonbonded pdb=" O LEU C 18 " pdb=" ND2 ASN A 37 " model vdw 2.239 2.520 nonbonded pdb=" O LEU I 18 " pdb=" ND2 ASN L 37 " model vdw 2.240 2.520 nonbonded pdb=" OE2 GLU A 34 " pdb=" NH1 ARG G 182 " model vdw 2.286 2.520 nonbonded pdb=" OE2 GLU H 34 " pdb=" NH1 ARG K 182 " model vdw 2.286 2.520 ... (remaining 179306 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'G' selection = chain 'H' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'C' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.010 Normalize map: mean=0, sd=1: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 6.780 Check model and map are aligned: 0.350 Set scattering table: 0.220 Process input model: 64.250 Find NCS groups from input model: 1.380 Set up NCS constraints: 0.170 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 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 : 0.009 0.074 23088 Z= 0.614 Angle : 1.236 16.028 31311 Z= 0.713 Chirality : 0.069 0.316 3408 Planarity : 0.008 0.083 4188 Dihedral : 12.443 72.574 8238 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.20 % Allowed : 14.81 % Favored : 84.98 % Rotamer: Outliers : 1.08 % Allowed : 11.04 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -5.02 (0.12), residues: 2943 helix: -4.31 (0.13), residues: 351 sheet: -2.81 (0.18), residues: 627 loop : -3.55 (0.11), residues: 1965 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP I 22 HIS 0.011 0.002 HIS I 272 PHE 0.029 0.003 PHE H 76 TYR 0.018 0.003 TYR F 178 ARG 0.017 0.002 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 714 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 690 time to evaluate : 2.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.8898 (tm-30) cc_final: 0.8652 (tm-30) REVERT: D 135 ASP cc_start: 0.7418 (t0) cc_final: 0.7046 (t0) REVERT: D 228 THR cc_start: 0.7844 (m) cc_final: 0.7577 (t) REVERT: D 853 THR cc_start: 0.9414 (m) cc_final: 0.8826 (p) REVERT: B 38 SER cc_start: 0.8824 (t) cc_final: 0.8533 (m) REVERT: B 58 ASP cc_start: 0.8955 (t0) cc_final: 0.8715 (t70) REVERT: A 58 ASP cc_start: 0.6083 (t0) cc_final: 0.5202 (t0) REVERT: A 73 LEU cc_start: 0.6695 (OUTLIER) cc_final: 0.6455 (pp) REVERT: A 76 PHE cc_start: 0.8537 (p90) cc_final: 0.7927 (p90) REVERT: E 61 GLN cc_start: 0.8728 (mm-40) cc_final: 0.8440 (mm-40) REVERT: E 83 GLU cc_start: 0.8992 (tm-30) cc_final: 0.8400 (tm-30) REVERT: E 99 TRP cc_start: 0.8829 (m100) cc_final: 0.8315 (m100) REVERT: F 74 ARG cc_start: 0.8705 (ptp-110) cc_final: 0.8500 (mtp-110) REVERT: F 135 ASP cc_start: 0.7313 (t0) cc_final: 0.6986 (t0) REVERT: F 220 ARG cc_start: 0.7646 (tpt170) cc_final: 0.7412 (tmt170) REVERT: F 853 THR cc_start: 0.9406 (m) cc_final: 0.8792 (p) REVERT: G 38 SER cc_start: 0.8937 (t) cc_final: 0.8704 (m) REVERT: G 208 VAL cc_start: 0.7731 (t) cc_final: 0.7257 (t) REVERT: H 58 ASP cc_start: 0.6260 (t0) cc_final: 0.5528 (t0) REVERT: H 73 LEU cc_start: 0.6417 (OUTLIER) cc_final: 0.6211 (pp) REVERT: H 178 ASP cc_start: 0.6184 (t0) cc_final: 0.5690 (t0) REVERT: I 54 MET cc_start: 0.6808 (mmm) cc_final: 0.6590 (mmm) REVERT: I 65 LEU cc_start: 0.8947 (mt) cc_final: 0.8744 (mm) REVERT: I 83 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8620 (tm-30) REVERT: J 135 ASP cc_start: 0.7402 (t0) cc_final: 0.7091 (t0) REVERT: J 220 ARG cc_start: 0.7555 (tpt170) cc_final: 0.7324 (tmt170) REVERT: J 768 SER cc_start: 0.8937 (p) cc_final: 0.8671 (t) REVERT: J 871 GLU cc_start: 0.7909 (tt0) cc_final: 0.7271 (tt0) REVERT: K 38 SER cc_start: 0.8887 (t) cc_final: 0.8588 (m) REVERT: K 58 ASP cc_start: 0.8936 (t0) cc_final: 0.8374 (t70) REVERT: L 58 ASP cc_start: 0.6040 (t0) cc_final: 0.5166 (t0) REVERT: L 73 LEU cc_start: 0.6505 (OUTLIER) cc_final: 0.6288 (pp) outliers start: 24 outliers final: 3 residues processed: 708 average time/residue: 0.4042 time to fit residues: 424.0878 Evaluate side-chains 425 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 419 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 248 optimal weight: 0.9980 chunk 222 optimal weight: 0.9980 chunk 123 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 150 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 230 optimal weight: 2.9990 chunk 89 optimal weight: 10.0000 chunk 140 optimal weight: 2.9990 chunk 171 optimal weight: 10.0000 chunk 266 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 10 HIS ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 232 GLN ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 4 HIS ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 42 HIS B 193 GLN A 74 HIS E 10 HIS ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN ** E 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN G 4 HIS G 42 HIS ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 4 HIS ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 HIS K 193 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 23088 Z= 0.259 Angle : 0.741 10.057 31311 Z= 0.389 Chirality : 0.047 0.207 3408 Planarity : 0.007 0.075 4188 Dihedral : 7.053 51.023 3305 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.99 % Favored : 88.01 % Rotamer: Outliers : 5.59 % Allowed : 17.16 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.12), residues: 2943 helix: -3.35 (0.18), residues: 354 sheet: -2.47 (0.19), residues: 561 loop : -3.11 (0.11), residues: 2028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 87 HIS 0.010 0.002 HIS H 74 PHE 0.044 0.002 PHE K 76 TYR 0.019 0.001 TYR J 794 ARG 0.007 0.001 ARG B 77 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 627 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 503 time to evaluate : 2.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8833 (p90) cc_final: 0.8155 (p90) REVERT: C 61 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8598 (mm-40) REVERT: C 69 ASN cc_start: 0.8751 (OUTLIER) cc_final: 0.8499 (m110) REVERT: D 135 ASP cc_start: 0.7209 (t0) cc_final: 0.6867 (t0) REVERT: D 178 TYR cc_start: 0.9029 (p90) cc_final: 0.8147 (p90) REVERT: D 220 ARG cc_start: 0.4486 (tmt170) cc_final: 0.4096 (tmt170) REVERT: D 871 GLU cc_start: 0.7955 (tt0) cc_final: 0.7693 (tt0) REVERT: B 38 SER cc_start: 0.8850 (t) cc_final: 0.8438 (m) REVERT: B 63 ILE cc_start: 0.9354 (pp) cc_final: 0.8895 (mt) REVERT: B 76 PHE cc_start: 0.8932 (p90) cc_final: 0.8679 (p90) REVERT: A 8 PHE cc_start: 0.7426 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: A 54 ARG cc_start: 0.6590 (mtt180) cc_final: 0.6372 (mtt180) REVERT: A 76 PHE cc_start: 0.8552 (p90) cc_final: 0.8260 (p90) REVERT: E 196 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.6145 (p90) REVERT: F 135 ASP cc_start: 0.6905 (t0) cc_final: 0.6688 (t0) REVERT: F 781 GLU cc_start: 0.7133 (tp30) cc_final: 0.6737 (tm-30) REVERT: F 823 GLN cc_start: 0.7777 (mp10) cc_final: 0.6412 (mm-40) REVERT: F 832 ARG cc_start: 0.7961 (mtm110) cc_final: 0.7665 (mtm110) REVERT: F 871 GLU cc_start: 0.7998 (tt0) cc_final: 0.7513 (tt0) REVERT: G 59 VAL cc_start: 0.9253 (t) cc_final: 0.9042 (p) REVERT: G 76 PHE cc_start: 0.8920 (p90) cc_final: 0.8700 (p90) REVERT: G 184 ASP cc_start: 0.8162 (t0) cc_final: 0.7535 (t0) REVERT: H 8 PHE cc_start: 0.7541 (OUTLIER) cc_final: 0.6443 (m-80) REVERT: H 76 PHE cc_start: 0.8499 (p90) cc_final: 0.8214 (p90) REVERT: I 102 ASN cc_start: 0.9076 (t0) cc_final: 0.8869 (t0) REVERT: I 140 GLN cc_start: 0.7639 (mt0) cc_final: 0.7291 (mt0) REVERT: J 79 MET cc_start: 0.8880 (tpt) cc_final: 0.8543 (tpt) REVERT: J 135 ASP cc_start: 0.7227 (t0) cc_final: 0.6797 (t0) REVERT: J 823 GLN cc_start: 0.7879 (mp10) cc_final: 0.6962 (mt0) REVERT: J 832 ARG cc_start: 0.7994 (mtp180) cc_final: 0.7673 (mtp180) REVERT: J 841 ASP cc_start: 0.7579 (t0) cc_final: 0.7366 (t0) REVERT: J 871 GLU cc_start: 0.7842 (tt0) cc_final: 0.6878 (tt0) REVERT: J 879 LYS cc_start: 0.8547 (mttt) cc_final: 0.7404 (mttt) REVERT: K 38 SER cc_start: 0.8752 (t) cc_final: 0.8494 (m) REVERT: K 63 ILE cc_start: 0.9325 (pp) cc_final: 0.8870 (mt) REVERT: K 76 PHE cc_start: 0.8722 (p90) cc_final: 0.8470 (p90) REVERT: L 8 PHE cc_start: 0.7526 (OUTLIER) cc_final: 0.7100 (m-80) outliers start: 124 outliers final: 59 residues processed: 584 average time/residue: 0.3170 time to fit residues: 293.5941 Evaluate side-chains 461 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 397 time to evaluate : 2.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain D residue 54 GLU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain A residue 8 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 256 THR Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 8 PHE Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 73 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 222 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 267 optimal weight: 2.9990 chunk 288 optimal weight: 9.9990 chunk 238 optimal weight: 0.0170 chunk 265 optimal weight: 3.9990 chunk 91 optimal weight: 8.9990 chunk 214 optimal weight: 9.9990 overall best weight: 3.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 764 GLN ** D 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 232 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 764 GLN ** K 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 23088 Z= 0.345 Angle : 0.770 12.869 31311 Z= 0.397 Chirality : 0.048 0.230 3408 Planarity : 0.006 0.071 4188 Dihedral : 6.829 52.832 3304 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.02 % Favored : 84.98 % Rotamer: Outliers : 6.85 % Allowed : 18.20 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -3.93 (0.13), residues: 2943 helix: -2.54 (0.22), residues: 348 sheet: -2.27 (0.20), residues: 507 loop : -2.92 (0.11), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 87 HIS 0.008 0.002 HIS H 74 PHE 0.032 0.002 PHE K 76 TYR 0.022 0.002 TYR J 794 ARG 0.008 0.001 ARG E 122 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 152 poor density : 420 time to evaluate : 2.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8705 (p90) cc_final: 0.8086 (p90) REVERT: C 196 PHE cc_start: 0.8393 (OUTLIER) cc_final: 0.7703 (p90) REVERT: D 135 ASP cc_start: 0.7442 (t0) cc_final: 0.7124 (t0) REVERT: D 841 ASP cc_start: 0.7779 (t0) cc_final: 0.7508 (t0) REVERT: D 871 GLU cc_start: 0.8025 (tt0) cc_final: 0.7811 (tt0) REVERT: D 938 THR cc_start: 0.9310 (OUTLIER) cc_final: 0.9075 (p) REVERT: B 35 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7858 (tm-30) REVERT: B 37 ASN cc_start: 0.8357 (t0) cc_final: 0.8116 (t0) REVERT: B 38 SER cc_start: 0.8952 (t) cc_final: 0.8579 (m) REVERT: B 184 ASP cc_start: 0.8291 (t0) cc_final: 0.7789 (t70) REVERT: B 191 SER cc_start: 0.7667 (p) cc_final: 0.7326 (p) REVERT: A 76 PHE cc_start: 0.8672 (p90) cc_final: 0.8471 (p90) REVERT: E 16 THR cc_start: 0.8763 (OUTLIER) cc_final: 0.8550 (p) REVERT: E 196 PHE cc_start: 0.8133 (OUTLIER) cc_final: 0.6797 (p90) REVERT: F 135 ASP cc_start: 0.7251 (t0) cc_final: 0.6989 (t0) REVERT: F 745 TRP cc_start: 0.6322 (p-90) cc_final: 0.5213 (p-90) REVERT: F 781 GLU cc_start: 0.7474 (tp30) cc_final: 0.6975 (tm-30) REVERT: F 823 GLN cc_start: 0.7933 (mp10) cc_final: 0.7134 (mt0) REVERT: F 841 ASP cc_start: 0.7776 (t0) cc_final: 0.7505 (t0) REVERT: F 871 GLU cc_start: 0.7915 (tt0) cc_final: 0.7419 (tt0) REVERT: G 67 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7483 (tm-30) REVERT: G 184 ASP cc_start: 0.8190 (t0) cc_final: 0.7597 (t0) REVERT: H 57 ASP cc_start: 0.8682 (t0) cc_final: 0.8405 (m-30) REVERT: H 178 ASP cc_start: 0.7675 (OUTLIER) cc_final: 0.7458 (t0) REVERT: H 194 SER cc_start: 0.8337 (t) cc_final: 0.7501 (m) REVERT: I 54 MET cc_start: 0.6294 (mmm) cc_final: 0.6063 (mmm) REVERT: I 185 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9262 (tt) REVERT: J 79 MET cc_start: 0.8690 (tpt) cc_final: 0.8402 (tpt) REVERT: J 135 ASP cc_start: 0.7376 (t0) cc_final: 0.7155 (t0) REVERT: J 820 ARG cc_start: 0.8425 (tpp80) cc_final: 0.8224 (tpp80) REVERT: J 844 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8340 (tp) REVERT: J 871 GLU cc_start: 0.7935 (tt0) cc_final: 0.6932 (tt0) REVERT: J 879 LYS cc_start: 0.8725 (mttt) cc_final: 0.7524 (mttt) REVERT: K 35 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7973 (tm-30) REVERT: K 38 SER cc_start: 0.8788 (t) cc_final: 0.8499 (m) REVERT: K 202 GLN cc_start: 0.7817 (mp10) cc_final: 0.7566 (mp10) REVERT: L 178 ASP cc_start: 0.7642 (OUTLIER) cc_final: 0.6959 (t70) outliers start: 152 outliers final: 93 residues processed: 531 average time/residue: 0.3348 time to fit residues: 276.3814 Evaluate side-chains 479 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 378 time to evaluate : 2.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 875 ASP Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 164 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 239 VAL Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 801 THR Chi-restraints excluded: chain J residue 811 LEU Chi-restraints excluded: chain J residue 844 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 264 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 138 optimal weight: 0.0040 chunk 29 optimal weight: 3.9990 chunk 127 optimal weight: 3.9990 chunk 179 optimal weight: 10.0000 chunk 268 optimal weight: 6.9990 chunk 284 optimal weight: 2.9990 chunk 140 optimal weight: 0.0070 chunk 254 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 overall best weight: 2.2016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 807 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 10 HIS ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 23088 Z= 0.274 Angle : 0.717 12.252 31311 Z= 0.369 Chirality : 0.047 0.277 3408 Planarity : 0.006 0.065 4188 Dihedral : 6.490 54.549 3302 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 19.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.63 % Favored : 86.37 % Rotamer: Outliers : 7.52 % Allowed : 19.86 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -3.70 (0.13), residues: 2943 helix: -2.11 (0.24), residues: 357 sheet: -2.13 (0.22), residues: 483 loop : -2.80 (0.11), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 87 HIS 0.007 0.001 HIS G 74 PHE 0.029 0.002 PHE K 76 TYR 0.020 0.001 TYR J 794 ARG 0.006 0.001 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 418 time to evaluate : 2.629 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8613 (p90) cc_final: 0.8187 (p90) REVERT: C 65 LEU cc_start: 0.9195 (mm) cc_final: 0.8885 (mm) REVERT: D 68 GLU cc_start: 0.8130 (mt-10) cc_final: 0.7908 (mt-10) REVERT: D 135 ASP cc_start: 0.7336 (t0) cc_final: 0.7018 (t0) REVERT: D 871 GLU cc_start: 0.8041 (tt0) cc_final: 0.7799 (tt0) REVERT: B 184 ASP cc_start: 0.8185 (t0) cc_final: 0.7759 (t70) REVERT: A 57 ASP cc_start: 0.8795 (t0) cc_final: 0.8571 (m-30) REVERT: E 54 MET cc_start: 0.6532 (mmm) cc_final: 0.5992 (mmm) REVERT: E 196 PHE cc_start: 0.8127 (OUTLIER) cc_final: 0.6929 (p90) REVERT: F 745 TRP cc_start: 0.6349 (p-90) cc_final: 0.5203 (p-90) REVERT: F 841 ASP cc_start: 0.7783 (t0) cc_final: 0.7502 (t0) REVERT: F 871 GLU cc_start: 0.7804 (tt0) cc_final: 0.7389 (tt0) REVERT: G 67 GLU cc_start: 0.7747 (tm-30) cc_final: 0.7401 (tm-30) REVERT: G 184 ASP cc_start: 0.8233 (t0) cc_final: 0.7645 (t0) REVERT: H 57 ASP cc_start: 0.8792 (t0) cc_final: 0.8487 (m-30) REVERT: H 178 ASP cc_start: 0.7649 (OUTLIER) cc_final: 0.7381 (t70) REVERT: H 194 SER cc_start: 0.8314 (t) cc_final: 0.7650 (m) REVERT: I 185 LEU cc_start: 0.9503 (OUTLIER) cc_final: 0.9275 (tt) REVERT: J 135 ASP cc_start: 0.7343 (t0) cc_final: 0.7043 (t0) REVERT: J 823 GLN cc_start: 0.7524 (mp10) cc_final: 0.6938 (mt0) REVERT: J 841 ASP cc_start: 0.7782 (t0) cc_final: 0.7518 (t0) REVERT: J 844 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8235 (tp) REVERT: J 871 GLU cc_start: 0.7863 (tt0) cc_final: 0.7102 (tt0) REVERT: K 35 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7890 (tm-30) REVERT: K 38 SER cc_start: 0.8746 (t) cc_final: 0.8471 (m) REVERT: L 54 ARG cc_start: 0.6438 (mtt-85) cc_final: 0.6051 (mtt180) REVERT: L 57 ASP cc_start: 0.8740 (t0) cc_final: 0.8384 (m-30) REVERT: L 178 ASP cc_start: 0.7600 (OUTLIER) cc_final: 0.7004 (t70) REVERT: L 194 SER cc_start: 0.8234 (t) cc_final: 0.7446 (m) outliers start: 167 outliers final: 100 residues processed: 542 average time/residue: 0.3287 time to fit residues: 278.7408 Evaluate side-chains 484 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 379 time to evaluate : 2.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 860 GLU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 160 ARG Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 160 ARG Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 844 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 17 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 190 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 236 optimal weight: 3.9990 chunk 161 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 211 optimal weight: 0.4980 chunk 117 optimal weight: 6.9990 chunk 242 optimal weight: 9.9990 chunk 196 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 145 optimal weight: 0.6980 chunk 255 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 823 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23088 Z= 0.213 Angle : 0.694 11.753 31311 Z= 0.352 Chirality : 0.046 0.282 3408 Planarity : 0.005 0.060 4188 Dihedral : 6.128 56.257 3302 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.15 % Favored : 86.85 % Rotamer: Outliers : 6.98 % Allowed : 21.62 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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 (0.13), residues: 2943 helix: -1.72 (0.26), residues: 339 sheet: -2.02 (0.22), residues: 483 loop : -2.69 (0.12), residues: 2121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP J 87 HIS 0.007 0.001 HIS G 74 PHE 0.037 0.002 PHE A 76 TYR 0.020 0.001 TYR J 794 ARG 0.004 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 426 time to evaluate : 2.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8527 (p90) cc_final: 0.8276 (p90) REVERT: C 65 LEU cc_start: 0.9127 (mm) cc_final: 0.8839 (mm) REVERT: C 69 ASN cc_start: 0.8725 (OUTLIER) cc_final: 0.8299 (m110) REVERT: D 135 ASP cc_start: 0.7304 (t0) cc_final: 0.7017 (t0) REVERT: D 220 ARG cc_start: 0.5193 (tmt170) cc_final: 0.4513 (ttp-170) REVERT: B 60 GLU cc_start: 0.8524 (mt-10) cc_final: 0.7898 (pt0) REVERT: B 184 ASP cc_start: 0.8009 (t0) cc_final: 0.7675 (t70) REVERT: A 57 ASP cc_start: 0.8695 (t0) cc_final: 0.8487 (m-30) REVERT: A 69 ARG cc_start: 0.6890 (ptp-170) cc_final: 0.6584 (ptm160) REVERT: E 196 PHE cc_start: 0.8060 (OUTLIER) cc_final: 0.6911 (p90) REVERT: F 75 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.9099 (pt) REVERT: F 745 TRP cc_start: 0.6314 (p-90) cc_final: 0.5232 (p-90) REVERT: F 841 ASP cc_start: 0.7779 (t0) cc_final: 0.7494 (t0) REVERT: F 871 GLU cc_start: 0.7726 (tt0) cc_final: 0.7437 (tt0) REVERT: G 4 HIS cc_start: 0.6354 (t70) cc_final: 0.6087 (t70) REVERT: G 184 ASP cc_start: 0.8160 (t0) cc_final: 0.7636 (t0) REVERT: H 35 GLU cc_start: 0.8914 (pm20) cc_final: 0.8646 (pm20) REVERT: H 57 ASP cc_start: 0.8764 (t0) cc_final: 0.8474 (m-30) REVERT: H 58 ASP cc_start: 0.6994 (t0) cc_final: 0.6787 (t0) REVERT: H 178 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7156 (t70) REVERT: I 54 MET cc_start: 0.6138 (mmm) cc_final: 0.5062 (mmm) REVERT: I 184 ARG cc_start: 0.8531 (tpp80) cc_final: 0.8225 (mmm-85) REVERT: I 185 LEU cc_start: 0.9477 (OUTLIER) cc_final: 0.9225 (tt) REVERT: J 135 ASP cc_start: 0.7345 (t0) cc_final: 0.7088 (t0) REVERT: J 823 GLN cc_start: 0.7415 (mp10) cc_final: 0.6895 (mt0) REVERT: J 844 LEU cc_start: 0.8481 (OUTLIER) cc_final: 0.8251 (tp) REVERT: J 853 THR cc_start: 0.9200 (m) cc_final: 0.8574 (p) REVERT: J 871 GLU cc_start: 0.7817 (tt0) cc_final: 0.7295 (tt0) REVERT: K 4 HIS cc_start: 0.6099 (t70) cc_final: 0.5638 (t-170) REVERT: K 5 GLU cc_start: 0.5596 (OUTLIER) cc_final: 0.5110 (tm-30) REVERT: K 35 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7933 (tm-30) REVERT: L 54 ARG cc_start: 0.6337 (mtt-85) cc_final: 0.6122 (mtt180) REVERT: L 57 ASP cc_start: 0.8735 (t0) cc_final: 0.8410 (m-30) REVERT: L 178 ASP cc_start: 0.7569 (OUTLIER) cc_final: 0.6735 (t0) REVERT: L 194 SER cc_start: 0.8447 (t) cc_final: 0.7805 (m) REVERT: L 195 PHE cc_start: 0.7673 (m-10) cc_final: 0.7424 (m-10) outliers start: 155 outliers final: 119 residues processed: 534 average time/residue: 0.3287 time to fit residues: 274.1257 Evaluate side-chains 519 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 392 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 25 GLU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain G residue 208 VAL Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 844 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 5 GLU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 95 optimal weight: 8.9990 chunk 255 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 166 optimal weight: 8.9990 chunk 70 optimal weight: 0.2980 chunk 284 optimal weight: 9.9990 chunk 236 optimal weight: 2.9990 chunk 131 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 72 GLN ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 23088 Z= 0.287 Angle : 0.716 11.992 31311 Z= 0.367 Chirality : 0.048 0.317 3408 Planarity : 0.005 0.062 4188 Dihedral : 6.252 57.075 3302 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 19.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.37 % Favored : 85.63 % Rotamer: Outliers : 7.21 % Allowed : 22.57 % Favored : 70.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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 (0.13), residues: 2943 helix: -1.68 (0.27), residues: 327 sheet: -2.02 (0.22), residues: 489 loop : -2.64 (0.12), residues: 2127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP I 22 HIS 0.006 0.001 HIS K 74 PHE 0.031 0.002 PHE L 76 TYR 0.022 0.002 TYR J 794 ARG 0.011 0.001 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 396 time to evaluate : 2.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 65 LEU cc_start: 0.9243 (mm) cc_final: 0.8957 (mm) REVERT: D 135 ASP cc_start: 0.7443 (t0) cc_final: 0.7060 (t0) REVERT: D 871 GLU cc_start: 0.7949 (tt0) cc_final: 0.7594 (tt0) REVERT: B 60 GLU cc_start: 0.8510 (mt-10) cc_final: 0.7838 (pt0) REVERT: B 184 ASP cc_start: 0.7975 (t0) cc_final: 0.7673 (t70) REVERT: A 35 GLU cc_start: 0.8827 (pm20) cc_final: 0.8413 (pm20) REVERT: A 57 ASP cc_start: 0.8753 (t0) cc_final: 0.8535 (m-30) REVERT: E 194 ARG cc_start: 0.8764 (ttm110) cc_final: 0.8374 (ttm170) REVERT: E 196 PHE cc_start: 0.8207 (OUTLIER) cc_final: 0.7008 (p90) REVERT: F 75 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9134 (pt) REVERT: F 79 MET cc_start: 0.8712 (mmm) cc_final: 0.8492 (mmm) REVERT: F 828 MET cc_start: 0.8955 (mmm) cc_final: 0.8520 (mmm) REVERT: F 841 ASP cc_start: 0.7866 (t0) cc_final: 0.7634 (t0) REVERT: G 4 HIS cc_start: 0.6239 (t70) cc_final: 0.6012 (t70) REVERT: G 60 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.7893 (pt0) REVERT: G 184 ASP cc_start: 0.8156 (t0) cc_final: 0.7588 (t0) REVERT: H 35 GLU cc_start: 0.8925 (pm20) cc_final: 0.8381 (pm20) REVERT: H 57 ASP cc_start: 0.8785 (t0) cc_final: 0.8484 (m-30) REVERT: H 73 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6270 (pp) REVERT: H 178 ASP cc_start: 0.7637 (OUTLIER) cc_final: 0.7247 (t70) REVERT: I 184 ARG cc_start: 0.8553 (tpp80) cc_final: 0.8238 (mmm-85) REVERT: I 185 LEU cc_start: 0.9489 (OUTLIER) cc_final: 0.9234 (tt) REVERT: J 135 ASP cc_start: 0.7475 (t0) cc_final: 0.7182 (t0) REVERT: J 823 GLN cc_start: 0.7417 (mp10) cc_final: 0.6941 (mt0) REVERT: J 844 LEU cc_start: 0.8589 (OUTLIER) cc_final: 0.8325 (tp) REVERT: J 853 THR cc_start: 0.9214 (m) cc_final: 0.8609 (p) REVERT: J 871 GLU cc_start: 0.7854 (tt0) cc_final: 0.7412 (tt0) REVERT: K 35 GLU cc_start: 0.8170 (tm-30) cc_final: 0.7823 (tm-30) REVERT: L 57 ASP cc_start: 0.8731 (t0) cc_final: 0.8446 (m-30) REVERT: L 76 PHE cc_start: 0.8223 (p90) cc_final: 0.7811 (p90) REVERT: L 178 ASP cc_start: 0.7582 (OUTLIER) cc_final: 0.6925 (t0) outliers start: 160 outliers final: 129 residues processed: 510 average time/residue: 0.3333 time to fit residues: 264.7359 Evaluate side-chains 505 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 368 time to evaluate : 2.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 929 LEU Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 17 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 120 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 176 ILE Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 5 GLU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 17 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 35 THR Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 120 VAL Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 842 LEU Chi-restraints excluded: chain J residue 844 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 200 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 274 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 162 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 160 optimal weight: 2.9990 chunk 239 optimal weight: 0.0370 chunk 158 optimal weight: 0.7980 chunk 283 optimal weight: 10.0000 chunk 177 optimal weight: 10.0000 chunk 172 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 overall best weight: 1.5062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 23088 Z= 0.220 Angle : 0.697 12.333 31311 Z= 0.356 Chirality : 0.047 0.345 3408 Planarity : 0.005 0.058 4188 Dihedral : 6.047 58.510 3302 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 17.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.25 % Favored : 86.75 % Rotamer: Outliers : 7.25 % Allowed : 23.87 % Favored : 68.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -3.27 (0.14), residues: 2943 helix: -1.39 (0.28), residues: 330 sheet: -1.92 (0.22), residues: 477 loop : -2.55 (0.12), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP J 87 HIS 0.005 0.001 HIS G 74 PHE 0.027 0.001 PHE L 76 TYR 0.021 0.001 TYR J 794 ARG 0.015 0.000 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 405 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8610 (p90) cc_final: 0.8348 (p90) REVERT: C 65 LEU cc_start: 0.9193 (mm) cc_final: 0.8928 (mm) REVERT: C 69 ASN cc_start: 0.8680 (OUTLIER) cc_final: 0.8316 (m110) REVERT: D 135 ASP cc_start: 0.7361 (t0) cc_final: 0.6985 (t0) REVERT: D 220 ARG cc_start: 0.5215 (tmt170) cc_final: 0.4478 (ttp-170) REVERT: B 60 GLU cc_start: 0.8501 (mt-10) cc_final: 0.7799 (pt0) REVERT: B 184 ASP cc_start: 0.7905 (t0) cc_final: 0.7662 (t70) REVERT: E 54 MET cc_start: 0.6272 (mmm) cc_final: 0.5624 (mmp) REVERT: E 194 ARG cc_start: 0.8760 (ttm110) cc_final: 0.8345 (ttm170) REVERT: F 75 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9088 (pt) REVERT: F 828 MET cc_start: 0.8943 (mmm) cc_final: 0.8537 (mmm) REVERT: F 841 ASP cc_start: 0.7788 (t0) cc_final: 0.7573 (t0) REVERT: G 4 HIS cc_start: 0.6266 (t70) cc_final: 0.6057 (t70) REVERT: G 184 ASP cc_start: 0.8118 (t0) cc_final: 0.7725 (t70) REVERT: H 34 GLU cc_start: 0.8099 (pt0) cc_final: 0.7813 (pt0) REVERT: H 57 ASP cc_start: 0.8773 (t0) cc_final: 0.8530 (m-30) REVERT: H 73 LEU cc_start: 0.7025 (OUTLIER) cc_final: 0.6323 (pp) REVERT: H 178 ASP cc_start: 0.7768 (OUTLIER) cc_final: 0.7314 (t70) REVERT: I 184 ARG cc_start: 0.8530 (tpp80) cc_final: 0.8227 (mmm-85) REVERT: I 185 LEU cc_start: 0.9472 (OUTLIER) cc_final: 0.9220 (tt) REVERT: J 135 ASP cc_start: 0.7418 (t0) cc_final: 0.7117 (t0) REVERT: J 841 ASP cc_start: 0.7767 (t0) cc_final: 0.7551 (t0) REVERT: J 844 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8263 (tp) REVERT: J 853 THR cc_start: 0.9199 (m) cc_final: 0.8592 (p) REVERT: K 35 GLU cc_start: 0.8229 (tm-30) cc_final: 0.7891 (tm-30) REVERT: K 182 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7635 (ppt-90) REVERT: L 54 ARG cc_start: 0.6584 (mtt180) cc_final: 0.6337 (mtt180) REVERT: L 57 ASP cc_start: 0.8760 (t0) cc_final: 0.8443 (m-30) REVERT: L 69 ARG cc_start: 0.5757 (ptm160) cc_final: 0.4834 (ptm160) REVERT: L 76 PHE cc_start: 0.8328 (p90) cc_final: 0.7899 (p90) REVERT: L 178 ASP cc_start: 0.7512 (OUTLIER) cc_final: 0.6660 (t0) outliers start: 161 outliers final: 124 residues processed: 519 average time/residue: 0.3399 time to fit residues: 274.7441 Evaluate side-chains 504 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 372 time to evaluate : 2.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain C residue 282 TYR Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain E residue 282 TYR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 844 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 900 LEU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 938 THR Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 29 LEU Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 182 ARG Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 208 VAL Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 175 optimal weight: 4.9990 chunk 113 optimal weight: 3.9990 chunk 169 optimal weight: 0.7980 chunk 85 optimal weight: 0.3980 chunk 55 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 180 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 140 optimal weight: 0.0070 chunk 26 optimal weight: 5.9990 chunk 222 optimal weight: 8.9990 overall best weight: 1.2402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.5024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23088 Z= 0.205 Angle : 0.700 12.496 31311 Z= 0.354 Chirality : 0.047 0.375 3408 Planarity : 0.005 0.054 4188 Dihedral : 5.916 59.222 3302 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.49 % Favored : 86.51 % Rotamer: Outliers : 6.53 % Allowed : 24.82 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -3.19 (0.14), residues: 2943 helix: -1.16 (0.28), residues: 345 sheet: -1.87 (0.22), residues: 495 loop : -2.53 (0.12), residues: 2103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP J 87 HIS 0.008 0.001 HIS L 46 PHE 0.025 0.001 PHE L 76 TYR 0.024 0.001 TYR E 73 ARG 0.009 0.000 ARG L 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 552 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 407 time to evaluate : 2.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8619 (p90) cc_final: 0.8385 (p90) REVERT: C 65 LEU cc_start: 0.9164 (mm) cc_final: 0.8904 (mm) REVERT: C 69 ASN cc_start: 0.8548 (OUTLIER) cc_final: 0.8164 (m110) REVERT: D 135 ASP cc_start: 0.7332 (t0) cc_final: 0.6982 (t0) REVERT: D 220 ARG cc_start: 0.5152 (tmt170) cc_final: 0.4416 (ttp-170) REVERT: B 60 GLU cc_start: 0.8336 (mt-10) cc_final: 0.7765 (pt0) REVERT: B 184 ASP cc_start: 0.7816 (t0) cc_final: 0.7548 (t70) REVERT: E 54 MET cc_start: 0.6168 (mmm) cc_final: 0.5529 (mmp) REVERT: E 277 ASP cc_start: 0.8066 (t0) cc_final: 0.7853 (t0) REVERT: F 75 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9072 (pt) REVERT: F 79 MET cc_start: 0.8680 (mmm) cc_final: 0.8477 (mmm) REVERT: F 841 ASP cc_start: 0.7778 (t0) cc_final: 0.7567 (t0) REVERT: G 4 HIS cc_start: 0.6428 (t70) cc_final: 0.6213 (t70) REVERT: G 61 ARG cc_start: 0.8191 (ptp-170) cc_final: 0.7749 (ptp-170) REVERT: G 184 ASP cc_start: 0.8064 (t0) cc_final: 0.7766 (t70) REVERT: H 54 ARG cc_start: 0.6656 (mtt180) cc_final: 0.6366 (mtt180) REVERT: H 57 ASP cc_start: 0.8782 (t0) cc_final: 0.8522 (m-30) REVERT: H 158 ILE cc_start: 0.8577 (mp) cc_final: 0.8332 (tt) REVERT: H 178 ASP cc_start: 0.7691 (OUTLIER) cc_final: 0.7246 (t70) REVERT: I 184 ARG cc_start: 0.8538 (tpp80) cc_final: 0.8263 (mmm-85) REVERT: I 185 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9229 (tt) REVERT: J 135 ASP cc_start: 0.7341 (t0) cc_final: 0.7016 (t0) REVERT: J 220 ARG cc_start: 0.4969 (OUTLIER) cc_final: 0.4350 (tmt170) REVERT: J 823 GLN cc_start: 0.7354 (mp10) cc_final: 0.7004 (pt0) REVERT: J 841 ASP cc_start: 0.7776 (t0) cc_final: 0.7568 (t0) REVERT: J 844 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8244 (tp) REVERT: J 853 THR cc_start: 0.9178 (m) cc_final: 0.8547 (p) REVERT: J 871 GLU cc_start: 0.8044 (tt0) cc_final: 0.7732 (tt0) REVERT: K 35 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7800 (tm-30) REVERT: L 76 PHE cc_start: 0.8286 (p90) cc_final: 0.7641 (p90) outliers start: 145 outliers final: 125 residues processed: 509 average time/residue: 0.3460 time to fit residues: 273.5857 Evaluate side-chains 510 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 379 time to evaluate : 2.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 35 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 176 ILE Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 924 THR Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 69 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 178 ASP Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 116 HIS Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 282 TYR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 75 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 220 ARG Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 844 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 900 LEU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 30 SER Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain K residue 185 THR Chi-restraints excluded: chain K residue 191 SER Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 257 optimal weight: 4.9990 chunk 271 optimal weight: 0.3980 chunk 247 optimal weight: 2.9990 chunk 264 optimal weight: 10.0000 chunk 158 optimal weight: 0.8980 chunk 115 optimal weight: 1.9990 chunk 207 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 249 optimal weight: 0.7980 chunk 263 optimal weight: 0.0970 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 764 GLN ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23088 Z= 0.189 Angle : 0.705 12.586 31311 Z= 0.353 Chirality : 0.047 0.430 3408 Planarity : 0.005 0.054 4188 Dihedral : 5.698 55.083 3302 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 16.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Rotamer: Outliers : 6.13 % Allowed : 25.68 % Favored : 68.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -3.13 (0.14), residues: 2943 helix: -1.10 (0.29), residues: 327 sheet: -1.89 (0.22), residues: 486 loop : -2.47 (0.12), residues: 2130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP J 87 HIS 0.006 0.001 HIS H 46 PHE 0.024 0.001 PHE L 76 TYR 0.021 0.001 TYR J 794 ARG 0.007 0.000 ARG H 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 419 time to evaluate : 2.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8607 (p90) cc_final: 0.8320 (p90) REVERT: C 65 LEU cc_start: 0.9031 (mm) cc_final: 0.8790 (mm) REVERT: C 69 ASN cc_start: 0.8413 (OUTLIER) cc_final: 0.8100 (m110) REVERT: D 135 ASP cc_start: 0.7295 (t0) cc_final: 0.6912 (t0) REVERT: D 220 ARG cc_start: 0.5066 (tmt170) cc_final: 0.4398 (ttp-170) REVERT: B 60 GLU cc_start: 0.8322 (mt-10) cc_final: 0.7751 (pt0) REVERT: B 184 ASP cc_start: 0.7806 (t0) cc_final: 0.7539 (t70) REVERT: E 196 PHE cc_start: 0.8373 (OUTLIER) cc_final: 0.6774 (p90) REVERT: F 75 LEU cc_start: 0.9277 (OUTLIER) cc_final: 0.9057 (pt) REVERT: G 61 ARG cc_start: 0.8248 (ptp-170) cc_final: 0.7810 (ptp-170) REVERT: G 184 ASP cc_start: 0.7976 (t0) cc_final: 0.7744 (t70) REVERT: H 57 ASP cc_start: 0.8765 (t0) cc_final: 0.8497 (m-30) REVERT: H 158 ILE cc_start: 0.8624 (mp) cc_final: 0.8409 (tt) REVERT: H 178 ASP cc_start: 0.7610 (OUTLIER) cc_final: 0.7063 (t0) REVERT: I 108 MET cc_start: 0.8135 (tpt) cc_final: 0.7433 (tpt) REVERT: I 184 ARG cc_start: 0.8487 (tpp80) cc_final: 0.8238 (mmm-85) REVERT: I 185 LEU cc_start: 0.9417 (OUTLIER) cc_final: 0.9187 (tt) REVERT: J 135 ASP cc_start: 0.7348 (t0) cc_final: 0.7046 (t0) REVERT: J 220 ARG cc_start: 0.4884 (OUTLIER) cc_final: 0.4232 (tmt170) REVERT: J 823 GLN cc_start: 0.7409 (mp10) cc_final: 0.7154 (pt0) REVERT: J 844 LEU cc_start: 0.8484 (OUTLIER) cc_final: 0.8229 (tp) REVERT: K 35 GLU cc_start: 0.8088 (tm-30) cc_final: 0.7684 (tm-30) REVERT: K 69 ARG cc_start: 0.6122 (OUTLIER) cc_final: 0.5729 (ptp-170) REVERT: L 73 LEU cc_start: 0.6410 (pt) cc_final: 0.4636 (tp) outliers start: 136 outliers final: 115 residues processed: 511 average time/residue: 0.3504 time to fit residues: 276.8888 Evaluate side-chains 507 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 384 time to evaluate : 2.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 73 LEU Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 242 ASP Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 220 ARG Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 844 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 900 LEU Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 173 optimal weight: 0.0040 chunk 279 optimal weight: 9.9990 chunk 170 optimal weight: 0.0470 chunk 132 optimal weight: 10.0000 chunk 194 optimal weight: 1.9990 chunk 292 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 233 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 180 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 overall best weight: 1.6096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 140 GLN ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23088 Z= 0.233 Angle : 0.739 15.043 31311 Z= 0.371 Chirality : 0.047 0.365 3408 Planarity : 0.005 0.058 4188 Dihedral : 5.774 52.571 3302 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.10 % Favored : 85.90 % Rotamer: Outliers : 5.99 % Allowed : 26.49 % Favored : 67.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -3.11 (0.14), residues: 2943 helix: -1.05 (0.29), residues: 327 sheet: -1.80 (0.22), residues: 492 loop : -2.48 (0.12), residues: 2124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP J 87 HIS 0.007 0.001 HIS L 46 PHE 0.025 0.001 PHE G 76 TYR 0.023 0.001 TYR J 794 ARG 0.011 0.000 ARG L 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5886 Ramachandran restraints generated. 2943 Oldfield, 0 Emsley, 2943 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 388 time to evaluate : 2.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 22 TRP cc_start: 0.8702 (p90) cc_final: 0.8367 (p90) REVERT: C 65 LEU cc_start: 0.9114 (mm) cc_final: 0.8882 (mm) REVERT: C 69 ASN cc_start: 0.8494 (OUTLIER) cc_final: 0.8180 (m110) REVERT: D 135 ASP cc_start: 0.7233 (t0) cc_final: 0.6773 (t0) REVERT: D 879 LYS cc_start: 0.8044 (mttt) cc_final: 0.7739 (mttp) REVERT: B 60 GLU cc_start: 0.8310 (mt-10) cc_final: 0.7697 (pt0) REVERT: B 184 ASP cc_start: 0.7784 (t0) cc_final: 0.7573 (t70) REVERT: E 196 PHE cc_start: 0.8484 (OUTLIER) cc_final: 0.7156 (p90) REVERT: E 277 ASP cc_start: 0.8023 (t0) cc_final: 0.7804 (t0) REVERT: F 75 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9091 (pt) REVERT: G 53 LEU cc_start: 0.5920 (OUTLIER) cc_final: 0.5590 (mt) REVERT: G 61 ARG cc_start: 0.8325 (ptp-170) cc_final: 0.7966 (ptp-170) REVERT: G 184 ASP cc_start: 0.7963 (t0) cc_final: 0.7742 (t70) REVERT: H 57 ASP cc_start: 0.8810 (t0) cc_final: 0.8471 (m-30) REVERT: H 178 ASP cc_start: 0.7598 (OUTLIER) cc_final: 0.7098 (t70) REVERT: I 108 MET cc_start: 0.8025 (tpt) cc_final: 0.7519 (tpt) REVERT: I 184 ARG cc_start: 0.8491 (tpp80) cc_final: 0.8240 (mmm-85) REVERT: I 185 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9205 (tt) REVERT: J 135 ASP cc_start: 0.7412 (t0) cc_final: 0.7123 (t0) REVERT: J 220 ARG cc_start: 0.5063 (OUTLIER) cc_final: 0.4479 (tmt170) REVERT: J 844 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8305 (tp) REVERT: K 35 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7669 (tm-30) REVERT: L 76 PHE cc_start: 0.8422 (p90) cc_final: 0.8166 (p90) REVERT: L 178 ASP cc_start: 0.7444 (OUTLIER) cc_final: 0.6959 (t0) outliers start: 133 outliers final: 121 residues processed: 482 average time/residue: 0.3372 time to fit residues: 252.7068 Evaluate side-chains 511 residues out of total 2238 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 381 time to evaluate : 2.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 68 ASP Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain C residue 76 LEU Chi-restraints excluded: chain C residue 116 HIS Chi-restraints excluded: chain C residue 204 LEU Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 242 ASP Chi-restraints excluded: chain C residue 250 CYS Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 280 VAL Chi-restraints excluded: chain D residue 6 LEU Chi-restraints excluded: chain D residue 45 LEU Chi-restraints excluded: chain D residue 84 GLN Chi-restraints excluded: chain D residue 132 VAL Chi-restraints excluded: chain D residue 189 PHE Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain D residue 782 ILE Chi-restraints excluded: chain D residue 801 THR Chi-restraints excluded: chain D residue 806 LEU Chi-restraints excluded: chain D residue 902 LEU Chi-restraints excluded: chain D residue 938 THR Chi-restraints excluded: chain D residue 982 VAL Chi-restraints excluded: chain D residue 983 GLU Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 ARG Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 183 PHE Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 31 SER Chi-restraints excluded: chain A residue 40 TRP Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 191 SER Chi-restraints excluded: chain E residue 16 THR Chi-restraints excluded: chain E residue 35 THR Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 76 LEU Chi-restraints excluded: chain E residue 101 VAL Chi-restraints excluded: chain E residue 135 THR Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 204 LEU Chi-restraints excluded: chain E residue 211 LEU Chi-restraints excluded: chain E residue 239 VAL Chi-restraints excluded: chain E residue 242 ASP Chi-restraints excluded: chain E residue 250 CYS Chi-restraints excluded: chain E residue 280 VAL Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 40 VAL Chi-restraints excluded: chain F residue 75 LEU Chi-restraints excluded: chain F residue 84 GLN Chi-restraints excluded: chain F residue 86 ILE Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 160 LYS Chi-restraints excluded: chain F residue 189 PHE Chi-restraints excluded: chain F residue 225 ILE Chi-restraints excluded: chain F residue 782 ILE Chi-restraints excluded: chain F residue 784 VAL Chi-restraints excluded: chain F residue 801 THR Chi-restraints excluded: chain F residue 842 LEU Chi-restraints excluded: chain F residue 851 VAL Chi-restraints excluded: chain F residue 860 GLU Chi-restraints excluded: chain F residue 902 LEU Chi-restraints excluded: chain F residue 924 THR Chi-restraints excluded: chain F residue 929 LEU Chi-restraints excluded: chain F residue 938 THR Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 29 LEU Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 53 LEU Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 58 ASP Chi-restraints excluded: chain G residue 69 ARG Chi-restraints excluded: chain G residue 77 ARG Chi-restraints excluded: chain G residue 183 PHE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 56 LEU Chi-restraints excluded: chain H residue 61 ARG Chi-restraints excluded: chain H residue 73 LEU Chi-restraints excluded: chain H residue 178 ASP Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 191 SER Chi-restraints excluded: chain H residue 200 LEU Chi-restraints excluded: chain H residue 203 VAL Chi-restraints excluded: chain I residue 16 THR Chi-restraints excluded: chain I residue 17 THR Chi-restraints excluded: chain I residue 69 ASN Chi-restraints excluded: chain I residue 76 LEU Chi-restraints excluded: chain I residue 101 VAL Chi-restraints excluded: chain I residue 116 HIS Chi-restraints excluded: chain I residue 121 SER Chi-restraints excluded: chain I residue 145 ILE Chi-restraints excluded: chain I residue 185 LEU Chi-restraints excluded: chain I residue 204 LEU Chi-restraints excluded: chain I residue 211 LEU Chi-restraints excluded: chain I residue 242 ASP Chi-restraints excluded: chain I residue 250 CYS Chi-restraints excluded: chain I residue 256 THR Chi-restraints excluded: chain J residue 6 LEU Chi-restraints excluded: chain J residue 84 GLN Chi-restraints excluded: chain J residue 86 ILE Chi-restraints excluded: chain J residue 132 VAL Chi-restraints excluded: chain J residue 189 PHE Chi-restraints excluded: chain J residue 220 ARG Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain J residue 782 ILE Chi-restraints excluded: chain J residue 784 VAL Chi-restraints excluded: chain J residue 844 LEU Chi-restraints excluded: chain J residue 860 GLU Chi-restraints excluded: chain J residue 900 LEU Chi-restraints excluded: chain J residue 902 LEU Chi-restraints excluded: chain J residue 983 GLU Chi-restraints excluded: chain K residue 8 PHE Chi-restraints excluded: chain K residue 21 GLU Chi-restraints excluded: chain K residue 69 ARG Chi-restraints excluded: chain K residue 73 LEU Chi-restraints excluded: chain K residue 183 PHE Chi-restraints excluded: chain L residue 31 SER Chi-restraints excluded: chain L residue 40 TRP Chi-restraints excluded: chain L residue 56 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 178 ASP Chi-restraints excluded: chain L residue 190 VAL Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain L residue 200 LEU Chi-restraints excluded: chain L residue 203 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 185 optimal weight: 0.7980 chunk 248 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 233 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 239 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 10 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 GLN ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 140 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 11 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 823 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.097399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.087098 restraints weight = 56195.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.089342 restraints weight = 30564.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.090815 restraints weight = 19070.245| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23088 Z= 0.301 Angle : 0.763 13.469 31311 Z= 0.388 Chirality : 0.049 0.440 3408 Planarity : 0.006 0.081 4188 Dihedral : 6.140 49.689 3302 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.58 % Favored : 85.42 % Rotamer: Outliers : 6.26 % Allowed : 26.53 % Favored : 67.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.11 % 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: -3.19 (0.14), residues: 2943 helix: -1.20 (0.29), residues: 327 sheet: -1.88 (0.23), residues: 477 loop : -2.52 (0.12), residues: 2139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP J 87 HIS 0.006 0.001 HIS E 272 PHE 0.027 0.002 PHE L 76 TYR 0.024 0.002 TYR J 794 ARG 0.017 0.001 ARG L 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5237.11 seconds wall clock time: 94 minutes 47.73 seconds (5687.73 seconds total)