Starting phenix.real_space_refine on Tue Jul 7 07:48:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vma_65181/07_2026/9vma_65181_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vma_65181/07_2026/9vma_65181.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vma_65181/07_2026/9vma_65181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vma_65181/07_2026/9vma_65181.map" model { file = "/net/cci-nas-00/data/ceres_data/9vma_65181/07_2026/9vma_65181_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vma_65181/07_2026/9vma_65181_neut.cif" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.027 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: 6 Type Number sf(0) Gaussians P 1005 5.49 5 Mg 12 5.21 5 S 54 5.16 5 C 25179 2.51 5 N 7896 2.21 5 O 11460 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 45606 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4080 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 477} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4080 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 477} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4080 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 477} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4080 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 477} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4080 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 477} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 4080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 496, 4080 Classifications: {'peptide': 496} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 18, 'TRANS': 477} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 3455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 3455 Classifications: {'RNA': 163} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 18, 'rna3p_pur': 67, 'rna3p_pyr': 69} Link IDs: {'rna2p': 26, 'rna3p': 136} Chain breaks: 2 Chain: "H" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3395 Classifications: {'RNA': 160} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 13, 'rna3p_pur': 68, 'rna3p_pyr': 71} Link IDs: {'rna2p': 20, 'rna3p': 139} Chain breaks: 3 Chain: "I" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3395 Classifications: {'RNA': 160} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 15, 'rna3p_pur': 68, 'rna3p_pyr': 69} Link IDs: {'rna2p': 22, 'rna3p': 137} Chain breaks: 3 Chain: "J" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3395 Classifications: {'RNA': 160} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 68, 'rna3p_pyr': 70} Link IDs: {'rna2p': 21, 'rna3p': 138} Chain breaks: 3 Chain: "K" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3395 Classifications: {'RNA': 160} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 68, 'rna3p_pyr': 70} Link IDs: {'rna2p': 21, 'rna3p': 138} Chain breaks: 3 Chain: "L" Number of atoms: 3395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3395 Classifications: {'RNA': 160} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 14, 'rna3p_pur': 68, 'rna3p_pyr': 70} Link IDs: {'rna2p': 21, 'rna3p': 138} Chain breaks: 3 Chain: "M" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "N" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "O" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "P" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "Q" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "R" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 84 Classifications: {'DNA': 4} Link IDs: {'rna3p': 3} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {' MG': 1, 'DTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.92, per 1000 atoms: 0.20 Number of scatterers: 45606 At special positions: 0 Unit cell: (196.65, 176.7, 137.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 54 16.00 P 1005 15.00 Mg 12 11.99 O 11460 8.00 N 7896 7.00 C 25179 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5688 Finding SS restraints... Secondary structure from input PDB file: 145 helices and 18 sheets defined 61.9% alpha, 7.5% beta 316 base pairs and 551 stacking pairs defined. Time for finding SS restraints: 6.16 Creating SS restraints... Processing helix chain 'A' and resid 1 through 41 Processing helix chain 'A' and resid 42 through 44 No H-bonds generated for 'chain 'A' and resid 42 through 44' Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 58 through 61 Processing helix chain 'A' and resid 62 through 69 Processing helix chain 'A' and resid 69 through 83 removed outlier: 3.949A pdb=" N ILE A 73 " --> pdb=" O ASN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 110 through 129 Processing helix chain 'A' and resid 144 through 159 removed outlier: 3.504A pdb=" N ALA A 148 " --> pdb=" O ASN A 144 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASN A 159 " --> pdb=" O ASP A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 176 removed outlier: 3.863A pdb=" N SER A 175 " --> pdb=" O PHE A 172 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE A 176 " --> pdb=" O PHE A 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 176' Processing helix chain 'A' and resid 177 through 185 removed outlier: 3.576A pdb=" N PHE A 185 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 204 Processing helix chain 'A' and resid 216 through 226 removed outlier: 3.701A pdb=" N CYS A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 253 through 272 Processing helix chain 'A' and resid 316 through 336 Processing helix chain 'A' and resid 337 through 341 removed outlier: 3.592A pdb=" N LYS A 341 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 355 through 370 Processing helix chain 'A' and resid 374 through 383 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 403 through 432 Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.895A pdb=" N LEU A 444 " --> pdb=" O PHE A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 456 Processing helix chain 'A' and resid 468 through 484 removed outlier: 3.777A pdb=" N ILE A 472 " --> pdb=" O SER A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 489 Processing helix chain 'B' and resid 2 through 41 Processing helix chain 'B' and resid 42 through 44 No H-bonds generated for 'chain 'B' and resid 42 through 44' Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 58 through 61 Processing helix chain 'B' and resid 62 through 69 Processing helix chain 'B' and resid 69 through 83 removed outlier: 3.964A pdb=" N ILE B 73 " --> pdb=" O ASN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 129 Processing helix chain 'B' and resid 144 through 159 removed outlier: 3.528A pdb=" N ALA B 148 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ASN B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 176 removed outlier: 3.752A pdb=" N SER B 175 " --> pdb=" O PHE B 172 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ILE B 176 " --> pdb=" O PHE B 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 176' Processing helix chain 'B' and resid 177 through 185 Processing helix chain 'B' and resid 193 through 204 Processing helix chain 'B' and resid 215 through 226 removed outlier: 3.895A pdb=" N LEU B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 220 " --> pdb=" O SER B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.516A pdb=" N GLY B 237 " --> pdb=" O LEU B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 272 Processing helix chain 'B' and resid 316 through 336 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.615A pdb=" N LYS B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 370 Processing helix chain 'B' and resid 374 through 383 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 403 through 432 Processing helix chain 'B' and resid 439 through 444 removed outlier: 3.881A pdb=" N LEU B 444 " --> pdb=" O PHE B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 448 through 456 Processing helix chain 'B' and resid 468 through 483 removed outlier: 3.794A pdb=" N ILE B 472 " --> pdb=" O SER B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 484 through 489 Processing helix chain 'C' and resid 2 through 41 Processing helix chain 'C' and resid 42 through 44 No H-bonds generated for 'chain 'C' and resid 42 through 44' Processing helix chain 'C' and resid 52 through 56 Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 69 Processing helix chain 'C' and resid 69 through 83 removed outlier: 3.964A pdb=" N ILE C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 101 No H-bonds generated for 'chain 'C' and resid 99 through 101' Processing helix chain 'C' and resid 110 through 129 Processing helix chain 'C' and resid 144 through 159 removed outlier: 3.551A pdb=" N ALA C 148 " --> pdb=" O ASN C 144 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN C 159 " --> pdb=" O ASP C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 176 removed outlier: 3.793A pdb=" N SER C 175 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ILE C 176 " --> pdb=" O PHE C 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 176' Processing helix chain 'C' and resid 177 through 185 Processing helix chain 'C' and resid 193 through 204 Processing helix chain 'C' and resid 215 through 226 removed outlier: 3.614A pdb=" N CYS C 226 " --> pdb=" O ALA C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 removed outlier: 3.509A pdb=" N GLY C 237 " --> pdb=" O LEU C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 272 Processing helix chain 'C' and resid 316 through 336 Processing helix chain 'C' and resid 337 through 341 removed outlier: 3.622A pdb=" N LYS C 341 " --> pdb=" O PRO C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 355 through 370 Processing helix chain 'C' and resid 374 through 383 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 403 through 432 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.869A pdb=" N LEU C 444 " --> pdb=" O PHE C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 448 through 456 Processing helix chain 'C' and resid 468 through 483 removed outlier: 3.780A pdb=" N ILE C 472 " --> pdb=" O SER C 468 " (cutoff:3.500A) Processing helix chain 'C' and resid 484 through 489 removed outlier: 3.815A pdb=" N ILE C 488 " --> pdb=" O GLY C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 490 through 493 Processing helix chain 'D' and resid 2 through 41 Processing helix chain 'D' and resid 42 through 44 No H-bonds generated for 'chain 'D' and resid 42 through 44' Processing helix chain 'D' and resid 52 through 57 Processing helix chain 'D' and resid 58 through 61 Processing helix chain 'D' and resid 62 through 69 Processing helix chain 'D' and resid 69 through 83 removed outlier: 3.947A pdb=" N ILE D 73 " --> pdb=" O ASN D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 110 through 129 Processing helix chain 'D' and resid 144 through 159 removed outlier: 3.539A pdb=" N ALA D 148 " --> pdb=" O ASN D 144 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN D 159 " --> pdb=" O ASP D 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 185 Processing helix chain 'D' and resid 193 through 204 Processing helix chain 'D' and resid 215 through 226 removed outlier: 3.778A pdb=" N LEU D 219 " --> pdb=" O THR D 215 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS D 226 " --> pdb=" O ALA D 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 Processing helix chain 'D' and resid 253 through 272 Processing helix chain 'D' and resid 316 through 336 Processing helix chain 'D' and resid 337 through 341 removed outlier: 3.589A pdb=" N LYS D 341 " --> pdb=" O PRO D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 355 through 370 Processing helix chain 'D' and resid 374 through 383 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 403 through 432 Processing helix chain 'D' and resid 439 through 444 removed outlier: 3.902A pdb=" N LEU D 444 " --> pdb=" O PHE D 440 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 456 removed outlier: 3.592A pdb=" N LYS D 455 " --> pdb=" O ASP D 451 " (cutoff:3.500A) Processing helix chain 'D' and resid 468 through 483 removed outlier: 3.772A pdb=" N ILE D 472 " --> pdb=" O SER D 468 " (cutoff:3.500A) Processing helix chain 'D' and resid 484 through 493 Proline residue: D 491 - end of helix Processing helix chain 'E' and resid 2 through 41 Processing helix chain 'E' and resid 42 through 44 No H-bonds generated for 'chain 'E' and resid 42 through 44' Processing helix chain 'E' and resid 52 through 57 Processing helix chain 'E' and resid 58 through 61 Processing helix chain 'E' and resid 62 through 69 Processing helix chain 'E' and resid 69 through 83 removed outlier: 4.025A pdb=" N ILE E 73 " --> pdb=" O ASN E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 110 through 129 Processing helix chain 'E' and resid 144 through 159 removed outlier: 3.510A pdb=" N ALA E 148 " --> pdb=" O ASN E 144 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASN E 159 " --> pdb=" O ASP E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 176 removed outlier: 3.741A pdb=" N SER E 175 " --> pdb=" O PHE E 172 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 176 " --> pdb=" O PHE E 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 176' Processing helix chain 'E' and resid 177 through 185 Processing helix chain 'E' and resid 193 through 204 Processing helix chain 'E' and resid 215 through 226 removed outlier: 3.677A pdb=" N CYS E 226 " --> pdb=" O ALA E 222 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 237 Processing helix chain 'E' and resid 253 through 272 Processing helix chain 'E' and resid 316 through 336 Processing helix chain 'E' and resid 337 through 341 removed outlier: 3.637A pdb=" N LYS E 341 " --> pdb=" O PRO E 338 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 370 Processing helix chain 'E' and resid 374 through 383 Processing helix chain 'E' and resid 394 through 398 Processing helix chain 'E' and resid 403 through 432 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.913A pdb=" N LEU E 444 " --> pdb=" O PHE E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 448 through 456 removed outlier: 3.602A pdb=" N LYS E 455 " --> pdb=" O ASP E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 468 through 483 removed outlier: 3.794A pdb=" N ILE E 472 " --> pdb=" O SER E 468 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 493 removed outlier: 3.542A pdb=" N ILE E 488 " --> pdb=" O GLY E 484 " (cutoff:3.500A) Proline residue: E 491 - end of helix Processing helix chain 'F' and resid 2 through 41 Processing helix chain 'F' and resid 42 through 44 No H-bonds generated for 'chain 'F' and resid 42 through 44' Processing helix chain 'F' and resid 52 through 57 Processing helix chain 'F' and resid 58 through 61 Processing helix chain 'F' and resid 62 through 69 Processing helix chain 'F' and resid 69 through 83 removed outlier: 3.971A pdb=" N ILE F 73 " --> pdb=" O ASN F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 110 through 129 Processing helix chain 'F' and resid 144 through 159 removed outlier: 3.532A pdb=" N ALA F 148 " --> pdb=" O ASN F 144 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ASN F 159 " --> pdb=" O ASP F 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 removed outlier: 3.588A pdb=" N SER F 175 " --> pdb=" O PHE F 172 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ILE F 176 " --> pdb=" O PHE F 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 176' Processing helix chain 'F' and resid 177 through 185 Processing helix chain 'F' and resid 193 through 204 Processing helix chain 'F' and resid 215 through 226 removed outlier: 3.652A pdb=" N LEU F 219 " --> pdb=" O THR F 215 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 237 Processing helix chain 'F' and resid 253 through 272 Processing helix chain 'F' and resid 316 through 336 Processing helix chain 'F' and resid 337 through 341 removed outlier: 3.634A pdb=" N LYS F 341 " --> pdb=" O PRO F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 355 through 370 Processing helix chain 'F' and resid 374 through 383 Processing helix chain 'F' and resid 394 through 398 Processing helix chain 'F' and resid 403 through 432 Processing helix chain 'F' and resid 439 through 444 removed outlier: 3.914A pdb=" N LEU F 444 " --> pdb=" O PHE F 440 " (cutoff:3.500A) Processing helix chain 'F' and resid 448 through 456 removed outlier: 3.602A pdb=" N LYS F 455 " --> pdb=" O ASP F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 468 through 484 removed outlier: 3.834A pdb=" N ILE F 472 " --> pdb=" O SER F 468 " (cutoff:3.500A) Processing helix chain 'F' and resid 484 through 489 removed outlier: 3.642A pdb=" N ILE F 488 " --> pdb=" O GLY F 484 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 97 Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 243 removed outlier: 8.067A pdb=" N LYS A 298 " --> pdb=" O ILE A 283 " (cutoff:3.500A) removed outlier: 5.692A pdb=" N LEU A 285 " --> pdb=" O LYS A 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 300 through 303 Processing sheet with id=AA4, first strand: chain 'B' and resid 92 through 97 Processing sheet with id=AA5, first strand: chain 'B' and resid 239 through 243 removed outlier: 8.030A pdb=" N LYS B 298 " --> pdb=" O ILE B 283 " (cutoff:3.500A) removed outlier: 5.659A pdb=" N LEU B 285 " --> pdb=" O LYS B 298 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 300 through 303 Processing sheet with id=AA7, first strand: chain 'C' and resid 92 through 97 Processing sheet with id=AA8, first strand: chain 'C' and resid 239 through 243 removed outlier: 8.048A pdb=" N LYS C 298 " --> pdb=" O ILE C 283 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N LEU C 285 " --> pdb=" O LYS C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 300 through 303 Processing sheet with id=AB1, first strand: chain 'D' and resid 92 through 98 removed outlier: 3.758A pdb=" N LYS D 98 " --> pdb=" O GLY D 102 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 239 through 243 removed outlier: 3.508A pdb=" N GLY D 282 " --> pdb=" O GLU D 166 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N LYS D 298 " --> pdb=" O ILE D 283 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N LEU D 285 " --> pdb=" O LYS D 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 300 through 303 Processing sheet with id=AB4, first strand: chain 'E' and resid 92 through 97 Processing sheet with id=AB5, first strand: chain 'E' and resid 239 through 243 Processing sheet with id=AB6, first strand: chain 'E' and resid 300 through 303 Processing sheet with id=AB7, first strand: chain 'F' and resid 92 through 97 Processing sheet with id=AB8, first strand: chain 'F' and resid 239 through 243 Processing sheet with id=AB9, first strand: chain 'F' and resid 300 through 303 1410 hydrogen bonds defined for protein. 3996 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 732 hydrogen bonds 952 hydrogen bond angles 0 basepair planarities 316 basepair parallelities 551 stacking parallelities Total time for adding SS restraints: 9.32 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 8780 1.33 - 1.45: 16531 1.45 - 1.57: 21207 1.57 - 1.69: 1975 1.69 - 1.81: 78 Bond restraints: 48571 Sorted by residual: bond pdb=" N ASN B 490 " pdb=" CA ASN B 490 " ideal model delta sigma weight residual 1.462 1.493 -0.031 7.70e-03 1.69e+04 1.61e+01 bond pdb=" N ASN A 490 " pdb=" CA ASN A 490 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.55e+01 bond pdb=" N ASN C 490 " pdb=" CA ASN C 490 " ideal model delta sigma weight residual 1.462 1.492 -0.030 7.70e-03 1.69e+04 1.52e+01 bond pdb=" P DA N 3 " pdb=" O5' DA N 3 " ideal model delta sigma weight residual 1.593 1.630 -0.037 1.00e-02 1.00e+04 1.37e+01 bond pdb=" N LEU C 494 " pdb=" CA LEU C 494 " ideal model delta sigma weight residual 1.460 1.488 -0.027 8.20e-03 1.49e+04 1.11e+01 ... (remaining 48566 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 68978 2.71 - 5.42: 981 5.42 - 8.12: 264 8.12 - 10.83: 16 10.83 - 13.54: 1 Bond angle restraints: 70240 Sorted by residual: angle pdb=" PB DTP F 501 " pdb=" O3B DTP F 501 " pdb=" PG DTP F 501 " ideal model delta sigma weight residual 139.87 129.81 10.06 1.00e+00 1.00e+00 1.01e+02 angle pdb=" PB DTP A 501 " pdb=" O3B DTP A 501 " pdb=" PG DTP A 501 " ideal model delta sigma weight residual 139.87 130.00 9.87 1.00e+00 1.00e+00 9.75e+01 angle pdb=" PB DTP E 501 " pdb=" O3B DTP E 501 " pdb=" PG DTP E 501 " ideal model delta sigma weight residual 139.87 130.78 9.09 1.00e+00 1.00e+00 8.26e+01 angle pdb=" PB DTP C 501 " pdb=" O3B DTP C 501 " pdb=" PG DTP C 501 " ideal model delta sigma weight residual 139.87 131.12 8.75 1.00e+00 1.00e+00 7.65e+01 angle pdb=" PB DTP B 501 " pdb=" O3B DTP B 501 " pdb=" PG DTP B 501 " ideal model delta sigma weight residual 139.87 131.44 8.43 1.00e+00 1.00e+00 7.10e+01 ... (remaining 70235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.29: 27632 35.29 - 70.59: 2888 70.59 - 105.88: 282 105.88 - 141.17: 16 141.17 - 176.47: 31 Dihedral angle restraints: 30849 sinusoidal: 22053 harmonic: 8796 Sorted by residual: dihedral pdb=" C5' U G 127 " pdb=" C4' U G 127 " pdb=" C3' U G 127 " pdb=" O3' U G 127 " ideal model delta sinusoidal sigma weight residual 147.00 76.29 70.71 1 8.00e+00 1.56e-02 1.00e+02 dihedral pdb=" C5' U G 33 " pdb=" C4' U G 33 " pdb=" C3' U G 33 " pdb=" O3' U G 33 " ideal model delta sinusoidal sigma weight residual 82.00 148.67 -66.67 1 8.00e+00 1.56e-02 9.06e+01 dihedral pdb=" O4' U G 33 " pdb=" C4' U G 33 " pdb=" C3' U G 33 " pdb=" C2' U G 33 " ideal model delta sinusoidal sigma weight residual -35.00 30.51 -65.51 1 8.00e+00 1.56e-02 8.78e+01 ... (remaining 30846 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.137: 8084 0.137 - 0.275: 228 0.275 - 0.412: 4 0.412 - 0.549: 174 0.549 - 0.687: 27 Chirality restraints: 8517 Sorted by residual: chirality pdb=" P DA N 3 " pdb=" OP1 DA N 3 " pdb=" OP2 DA N 3 " pdb=" O5' DA N 3 " both_signs ideal model delta sigma weight residual True 2.34 -3.02 -0.69 2.00e-01 2.50e+01 1.18e+01 chirality pdb=" P DA O 4 " pdb=" OP1 DA O 4 " pdb=" OP2 DA O 4 " pdb=" O5' DA O 4 " both_signs ideal model delta sigma weight residual True 2.34 -3.00 -0.66 2.00e-01 2.50e+01 1.09e+01 chirality pdb=" P DA N 1 " pdb=" OP1 DA N 1 " pdb=" OP2 DA N 1 " pdb=" O5' DA N 1 " both_signs ideal model delta sigma weight residual True 2.34 -2.98 -0.65 2.00e-01 2.50e+01 1.04e+01 ... (remaining 8514 not shown) Planarity restraints: 5277 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG F 104 " 1.066 9.50e-02 1.11e+02 4.78e-01 1.38e+02 pdb=" NE ARG F 104 " -0.064 2.00e-02 2.50e+03 pdb=" CZ ARG F 104 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG F 104 " 0.007 2.00e-02 2.50e+03 pdb=" NH2 ARG F 104 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 140 " -0.294 9.50e-02 1.11e+02 1.32e-01 1.06e+01 pdb=" NE ARG B 140 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 140 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG B 140 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 140 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C I 108 " 0.034 2.00e-02 2.50e+03 1.76e-02 6.96e+00 pdb=" N1 C I 108 " -0.038 2.00e-02 2.50e+03 pdb=" C2 C I 108 " -0.003 2.00e-02 2.50e+03 pdb=" O2 C I 108 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C I 108 " 0.003 2.00e-02 2.50e+03 pdb=" C4 C I 108 " 0.002 2.00e-02 2.50e+03 pdb=" N4 C I 108 " 0.011 2.00e-02 2.50e+03 pdb=" C5 C I 108 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C I 108 " -0.004 2.00e-02 2.50e+03 ... (remaining 5274 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 12 2.06 - 2.77: 9355 2.77 - 3.48: 66576 3.48 - 4.19: 134173 4.19 - 4.90: 197335 Nonbonded interactions: 407451 Sorted by model distance: nonbonded pdb=" CE1 TYR F 243 " pdb=" OH TYR F 496 " model vdw 1.353 3.340 nonbonded pdb=" O PHE D 169 " pdb="MG MG D 502 " model vdw 1.768 2.170 nonbonded pdb=" ND1 HIS C 146 " pdb=" SD MET C 489 " model vdw 1.782 3.480 nonbonded pdb=" O PHE A 169 " pdb="MG MG A 502 " model vdw 1.816 2.170 nonbonded pdb=" O PHE F 169 " pdb="MG MG F 502 " model vdw 1.835 2.170 ... (remaining 407446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = (chain 'G' and (resid 1 through 124 or resid 128 through 201)) selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.800 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 40.920 Find NCS groups from input model: 0.920 Set up NCS constraints: 0.100 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 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 : 0.006 0.046 48571 Z= 0.356 Angle : 0.788 13.539 70240 Z= 0.494 Chirality : 0.087 0.687 8517 Planarity : 0.008 0.478 5277 Dihedral : 23.108 176.467 25161 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.07 % Allowed : 1.75 % Favored : 98.18 % Rotamer: Outliers : 2.56 % Allowed : 16.04 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.83 (0.16), residues: 2964 helix: 2.54 (0.13), residues: 1578 sheet: -2.20 (0.32), residues: 216 loop : 0.10 (0.20), residues: 1170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 39 TYR 0.022 0.001 TYR E 329 PHE 0.012 0.001 PHE F 120 TRP 0.009 0.001 TRP D 250 HIS 0.007 0.001 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.36 (48571) covalent geometry : angle 0.78849 / 0.49 (70240) hydrogen bonds : bond 0.16762 / 10.88 ( 2142) hydrogen bonds : angle 6.58136 / 4.75 ( 4948) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 489 time to evaluate : 1.031 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: A 218 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8487 (m) REVERT: A 392 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7777 (ptmt) REVERT: A 394 ILE cc_start: 0.9143 (tp) cc_final: 0.8893 (tp) REVERT: B 31 LEU cc_start: 0.9541 (tp) cc_final: 0.9337 (tt) REVERT: B 180 PHE cc_start: 0.8598 (t80) cc_final: 0.8071 (t80) REVERT: B 187 GLU cc_start: 0.8423 (mm-30) cc_final: 0.7875 (mm-30) REVERT: B 232 ASP cc_start: 0.8427 (m-30) cc_final: 0.8133 (m-30) REVERT: B 267 PHE cc_start: 0.8946 (t80) cc_final: 0.8691 (t80) REVERT: C 232 ASP cc_start: 0.8860 (m-30) cc_final: 0.8656 (m-30) REVERT: C 488 ILE cc_start: 0.8492 (mm) cc_final: 0.8197 (mm) REVERT: D 156 LEU cc_start: 0.9496 (mt) cc_final: 0.9280 (mp) REVERT: E 155 ASP cc_start: 0.8420 (t70) cc_final: 0.7755 (t0) REVERT: E 291 LEU cc_start: 0.6929 (OUTLIER) cc_final: 0.6556 (tp) REVERT: F 285 LEU cc_start: 0.9194 (tp) cc_final: 0.8987 (tp) REVERT: F 288 LYS cc_start: 0.8337 (mtpp) cc_final: 0.8115 (mmmt) outliers start: 69 outliers final: 17 residues processed: 540 average time/residue: 0.2605 time to fit residues: 229.3663 Evaluate side-chains 241 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 221 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 489 MET Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 251 SER Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 489 MET Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain E residue 251 SER Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 197 optimal weight: 4.9990 chunk 388 optimal weight: 50.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 6.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 223 ASN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 231 GLN ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN C 262 ASN C 334 ASN C 490 ASN D 150 GLN D 252 GLN D 477 GLN D 495 ASN E 213 GLN E 231 GLN E 252 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 377 GLN F 252 GLN F 439 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.070215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.050987 restraints weight = 223636.587| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 3.32 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 48571 Z= 0.168 Angle : 0.560 9.471 70240 Z= 0.322 Chirality : 0.038 0.305 8517 Planarity : 0.004 0.079 5277 Dihedral : 23.939 174.943 18886 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.63 % Allowed : 17.67 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 2964 helix: 2.46 (0.13), residues: 1596 sheet: -1.77 (0.33), residues: 216 loop : 0.06 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG D 205 TYR 0.024 0.002 TYR B 329 PHE 0.018 0.001 PHE C 303 TRP 0.011 0.001 TRP C 227 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.17 (48571) covalent geometry : angle 0.55999 / 0.32 (70240) hydrogen bonds : bond 0.08796 / 5.67 ( 2142) hydrogen bonds : angle 4.73349 / 3.40 ( 4948) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 244 time to evaluate : 0.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8678 (mt) REVERT: A 196 GLU cc_start: 0.8706 (mt-10) cc_final: 0.8486 (mt-10) REVERT: A 232 ASP cc_start: 0.8941 (t70) cc_final: 0.8639 (t70) REVERT: A 284 SER cc_start: 0.8994 (OUTLIER) cc_final: 0.8726 (t) REVERT: A 392 LYS cc_start: 0.8034 (OUTLIER) cc_final: 0.7487 (ptmt) REVERT: B 31 LEU cc_start: 0.9718 (tp) cc_final: 0.9517 (tt) REVERT: B 187 GLU cc_start: 0.8600 (mm-30) cc_final: 0.8159 (mm-30) REVERT: B 188 ASN cc_start: 0.8241 (t0) cc_final: 0.7822 (t0) REVERT: B 232 ASP cc_start: 0.8723 (m-30) cc_final: 0.8312 (m-30) REVERT: B 267 PHE cc_start: 0.8853 (t80) cc_final: 0.8619 (t80) REVERT: C 1 MET cc_start: 0.8456 (tmm) cc_final: 0.8092 (tmm) REVERT: C 144 ASN cc_start: 0.8171 (OUTLIER) cc_final: 0.7916 (p0) REVERT: C 228 LYS cc_start: 0.9157 (tppp) cc_final: 0.8732 (tppt) REVERT: C 232 ASP cc_start: 0.8859 (m-30) cc_final: 0.8629 (m-30) REVERT: C 364 GLU cc_start: 0.9187 (tp30) cc_final: 0.8942 (tp30) REVERT: D 8 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8305 (mp10) REVERT: D 16 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9162 (mttp) REVERT: D 156 LEU cc_start: 0.9752 (mt) cc_final: 0.9496 (mp) REVERT: D 196 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8419 (mt-10) REVERT: E 155 ASP cc_start: 0.8751 (OUTLIER) cc_final: 0.7930 (t0) REVERT: E 167 PHE cc_start: 0.8502 (m-80) cc_final: 0.8121 (m-80) REVERT: E 231 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8213 (tm-30) REVERT: E 251 SER cc_start: 0.9107 (t) cc_final: 0.8816 (p) REVERT: E 252 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8613 (mm-40) REVERT: F 155 ASP cc_start: 0.8618 (OUTLIER) cc_final: 0.8080 (t0) REVERT: F 166 GLU cc_start: 0.6333 (tm-30) cc_final: 0.5699 (tm-30) REVERT: F 235 ARG cc_start: 0.8922 (mtp85) cc_final: 0.8632 (mtp85) REVERT: F 279 LYS cc_start: 0.8436 (mtpt) cc_final: 0.8170 (mtmt) REVERT: F 403 ASP cc_start: 0.8788 (t0) cc_final: 0.8434 (t0) outliers start: 98 outliers final: 39 residues processed: 319 average time/residue: 0.2436 time to fit residues: 132.2387 Evaluate side-chains 250 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 201 time to evaluate : 1.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain A residue 496 TYR Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 231 GLN Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 252 GLN Chi-restraints excluded: chain E residue 284 SER Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 179 SER Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 385 optimal weight: 30.0000 chunk 192 optimal weight: 5.9990 chunk 383 optimal weight: 30.0000 chunk 113 optimal weight: 6.9990 chunk 165 optimal weight: 0.9990 chunk 147 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 224 optimal weight: 5.9990 chunk 328 optimal weight: 50.0000 chunk 105 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 GLN C 150 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 477 GLN E 231 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.068957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.050132 restraints weight = 220211.889| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.36 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 48571 Z= 0.172 Angle : 0.518 9.712 70240 Z= 0.301 Chirality : 0.037 0.304 8517 Planarity : 0.004 0.067 5277 Dihedral : 23.842 176.061 18873 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.41 % Allowed : 18.00 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 2964 helix: 2.48 (0.13), residues: 1596 sheet: -1.83 (0.29), residues: 252 loop : 0.10 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 28 TYR 0.022 0.002 TYR B 329 PHE 0.018 0.001 PHE A 391 TRP 0.012 0.001 TRP C 250 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 (48571) covalent geometry : angle 0.51792 / 0.30 (70240) hydrogen bonds : bond 0.07745 / 5.01 ( 2142) hydrogen bonds : angle 4.50649 / 3.24 ( 4948) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 217 time to evaluate : 1.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8671 (mt-10) cc_final: 0.8438 (mt-10) REVERT: A 196 GLU cc_start: 0.8762 (mt-10) cc_final: 0.8521 (mt-10) REVERT: A 232 ASP cc_start: 0.8997 (t70) cc_final: 0.8636 (t0) REVERT: A 284 SER cc_start: 0.9025 (OUTLIER) cc_final: 0.8756 (t) REVERT: A 289 LYS cc_start: 0.9268 (tppt) cc_final: 0.8981 (mmmt) REVERT: A 392 LYS cc_start: 0.7994 (OUTLIER) cc_final: 0.7367 (ptmt) REVERT: B 31 LEU cc_start: 0.9721 (tp) cc_final: 0.9516 (tt) REVERT: B 184 GLN cc_start: 0.8499 (OUTLIER) cc_final: 0.8149 (tt0) REVERT: B 187 GLU cc_start: 0.8663 (mm-30) cc_final: 0.8140 (mm-30) REVERT: B 228 LYS cc_start: 0.9125 (tppt) cc_final: 0.8731 (tppt) REVERT: B 232 ASP cc_start: 0.8775 (m-30) cc_final: 0.8290 (m-30) REVERT: B 267 PHE cc_start: 0.8839 (t80) cc_final: 0.8584 (t80) REVERT: C 1 MET cc_start: 0.8234 (tmm) cc_final: 0.7747 (tmm) REVERT: C 232 ASP cc_start: 0.8905 (m-30) cc_final: 0.8507 (m-30) REVERT: C 364 GLU cc_start: 0.9233 (tp30) cc_final: 0.9000 (tp30) REVERT: D 8 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8442 (mp10) REVERT: D 16 LYS cc_start: 0.9450 (OUTLIER) cc_final: 0.9116 (mttp) REVERT: D 95 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8585 (p0) REVERT: D 156 LEU cc_start: 0.9747 (mt) cc_final: 0.9532 (mp) REVERT: D 181 LEU cc_start: 0.9147 (OUTLIER) cc_final: 0.8892 (tp) REVERT: D 196 GLU cc_start: 0.8802 (mt-10) cc_final: 0.8350 (mt-10) REVERT: D 477 GLN cc_start: 0.8369 (mm110) cc_final: 0.8049 (mm110) REVERT: E 113 ASP cc_start: 0.9498 (m-30) cc_final: 0.9159 (m-30) REVERT: E 155 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8072 (t0) REVERT: E 232 ASP cc_start: 0.9003 (m-30) cc_final: 0.8753 (m-30) REVERT: E 251 SER cc_start: 0.9038 (t) cc_final: 0.8730 (p) REVERT: F 155 ASP cc_start: 0.8701 (OUTLIER) cc_final: 0.8288 (t0) REVERT: F 166 GLU cc_start: 0.6546 (tm-30) cc_final: 0.5945 (tm-30) REVERT: F 235 ARG cc_start: 0.8979 (mtp85) cc_final: 0.8699 (mtp85) REVERT: F 403 ASP cc_start: 0.8810 (t0) cc_final: 0.8419 (t0) REVERT: F 482 GLU cc_start: 0.9085 (OUTLIER) cc_final: 0.8733 (mp0) outliers start: 92 outliers final: 50 residues processed: 288 average time/residue: 0.2273 time to fit residues: 114.1740 Evaluate side-chains 249 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 189 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 184 GLN Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 224 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 253 GLU Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 233 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 241 SER Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 303 optimal weight: 40.0000 chunk 87 optimal weight: 9.9990 chunk 363 optimal weight: 40.0000 chunk 80 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 377 optimal weight: 50.0000 chunk 212 optimal weight: 5.9990 chunk 239 optimal weight: 20.0000 chunk 223 optimal weight: 40.0000 chunk 287 optimal weight: 1.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 5 GLN E 252 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 252 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.068091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.049292 restraints weight = 221545.906| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 3.35 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 48571 Z= 0.171 Angle : 0.509 10.176 70240 Z= 0.293 Chirality : 0.037 0.300 8517 Planarity : 0.004 0.067 5277 Dihedral : 23.786 177.992 18870 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.19 % Allowed : 18.56 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.16), residues: 2964 helix: 2.42 (0.13), residues: 1644 sheet: -1.86 (0.28), residues: 252 loop : 0.11 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 446 TYR 0.023 0.002 TYR E 381 PHE 0.026 0.002 PHE B 180 TRP 0.012 0.001 TRP C 413 HIS 0.009 0.002 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.17 (48571) covalent geometry : angle 0.50935 / 0.29 (70240) hydrogen bonds : bond 0.07106 / 4.59 ( 2142) hydrogen bonds : angle 4.37030 / 3.13 ( 4948) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 215 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 181 LEU cc_start: 0.9442 (tp) cc_final: 0.9214 (tt) REVERT: A 187 GLU cc_start: 0.8638 (mt-10) cc_final: 0.8437 (mt-10) REVERT: A 196 GLU cc_start: 0.8728 (mt-10) cc_final: 0.8492 (mt-10) REVERT: A 232 ASP cc_start: 0.9065 (t0) cc_final: 0.8730 (t0) REVERT: A 235 ARG cc_start: 0.8279 (mtt180) cc_final: 0.8014 (mtt180) REVERT: A 263 ILE cc_start: 0.9435 (mm) cc_final: 0.9145 (mt) REVERT: A 284 SER cc_start: 0.8974 (OUTLIER) cc_final: 0.8696 (t) REVERT: A 289 LYS cc_start: 0.9275 (tppt) cc_final: 0.8977 (mmmt) REVERT: A 392 LYS cc_start: 0.7691 (OUTLIER) cc_final: 0.7034 (ptmt) REVERT: B 31 LEU cc_start: 0.9731 (tp) cc_final: 0.9521 (tt) REVERT: B 187 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8208 (mp0) REVERT: B 228 LYS cc_start: 0.9179 (tppt) cc_final: 0.8818 (tppt) REVERT: B 232 ASP cc_start: 0.8795 (m-30) cc_final: 0.8278 (m-30) REVERT: B 236 GLU cc_start: 0.9119 (tp30) cc_final: 0.8556 (tp30) REVERT: B 392 LYS cc_start: 0.8288 (OUTLIER) cc_final: 0.7859 (ptmt) REVERT: C 232 ASP cc_start: 0.8855 (m-30) cc_final: 0.8595 (m-30) REVERT: C 364 GLU cc_start: 0.9217 (tp30) cc_final: 0.8966 (tp30) REVERT: C 440 PHE cc_start: 0.9305 (t80) cc_final: 0.8983 (t80) REVERT: D 8 GLN cc_start: 0.8784 (OUTLIER) cc_final: 0.8478 (mp10) REVERT: D 16 LYS cc_start: 0.9464 (OUTLIER) cc_final: 0.9066 (mtmp) REVERT: D 95 ASP cc_start: 0.8975 (OUTLIER) cc_final: 0.8478 (p0) REVERT: D 196 GLU cc_start: 0.8814 (mt-10) cc_final: 0.8293 (mt-10) REVERT: D 259 ASN cc_start: 0.9088 (m-40) cc_final: 0.8825 (m-40) REVERT: E 113 ASP cc_start: 0.9499 (m-30) cc_final: 0.9190 (m-30) REVERT: E 155 ASP cc_start: 0.8932 (t70) cc_final: 0.8246 (t0) REVERT: E 232 ASP cc_start: 0.9011 (m-30) cc_final: 0.8776 (m-30) REVERT: E 251 SER cc_start: 0.9106 (t) cc_final: 0.8894 (p) REVERT: E 489 MET cc_start: 0.7462 (OUTLIER) cc_final: 0.6968 (ptm) REVERT: F 129 ARG cc_start: 0.9151 (ptt-90) cc_final: 0.8750 (ptp90) REVERT: F 133 SER cc_start: 0.9169 (t) cc_final: 0.8842 (t) REVERT: F 166 GLU cc_start: 0.6633 (tm-30) cc_final: 0.5994 (tm-30) REVERT: F 224 LEU cc_start: 0.9577 (tt) cc_final: 0.9349 (pp) REVERT: F 235 ARG cc_start: 0.8865 (mtp85) cc_final: 0.8628 (mtp85) REVERT: F 257 ILE cc_start: 0.9418 (OUTLIER) cc_final: 0.8965 (tp) REVERT: F 403 ASP cc_start: 0.8878 (t0) cc_final: 0.8506 (t0) REVERT: F 482 GLU cc_start: 0.9089 (OUTLIER) cc_final: 0.8716 (mp0) outliers start: 113 outliers final: 60 residues processed: 302 average time/residue: 0.2252 time to fit residues: 117.4627 Evaluate side-chains 257 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 188 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 177 SER Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 392 LYS Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 470 LEU Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 264 ILE Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 248 ILE Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 482 GLU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 36 optimal weight: 5.9990 chunk 130 optimal weight: 3.9990 chunk 305 optimal weight: 30.0000 chunk 188 optimal weight: 6.9990 chunk 223 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 206 optimal weight: 4.9990 chunk 367 optimal weight: 40.0000 chunk 12 optimal weight: 4.9990 chunk 151 optimal weight: 9.9990 chunk 196 optimal weight: 10.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 259 ASN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.068268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.048861 restraints weight = 224310.200| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 3.34 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 48571 Z= 0.157 Angle : 0.493 11.397 70240 Z= 0.283 Chirality : 0.036 0.285 8517 Planarity : 0.004 0.064 5277 Dihedral : 23.759 178.553 18865 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.70 % Allowed : 19.15 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.16), residues: 2964 helix: 2.46 (0.13), residues: 1644 sheet: -1.77 (0.28), residues: 252 loop : 0.11 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 39 TYR 0.023 0.001 TYR E 381 PHE 0.016 0.001 PHE F 92 TRP 0.009 0.001 TRP C 250 HIS 0.008 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (48571) covalent geometry : angle 0.49293 / 0.28 (70240) hydrogen bonds : bond 0.06817 / 4.40 ( 2142) hydrogen bonds : angle 4.28184 / 3.06 ( 4948) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 200 time to evaluate : 1.291 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8712 (mt-10) cc_final: 0.8476 (mt-10) REVERT: A 232 ASP cc_start: 0.9070 (t0) cc_final: 0.8771 (t0) REVERT: A 284 SER cc_start: 0.9014 (m) cc_final: 0.8750 (t) REVERT: A 289 LYS cc_start: 0.9259 (tppt) cc_final: 0.8964 (mmmt) REVERT: A 392 LYS cc_start: 0.7572 (OUTLIER) cc_final: 0.7115 (ptmm) REVERT: B 31 LEU cc_start: 0.9732 (tp) cc_final: 0.9525 (tt) REVERT: B 155 ASP cc_start: 0.8929 (OUTLIER) cc_final: 0.8709 (t70) REVERT: B 187 GLU cc_start: 0.8792 (mm-30) cc_final: 0.8261 (mp0) REVERT: B 228 LYS cc_start: 0.9183 (tppt) cc_final: 0.8831 (tppt) REVERT: B 232 ASP cc_start: 0.8751 (m-30) cc_final: 0.8250 (m-30) REVERT: B 236 GLU cc_start: 0.9106 (tp30) cc_final: 0.8529 (tp30) REVERT: C 4 GLU cc_start: 0.9208 (tt0) cc_final: 0.8930 (tm-30) REVERT: C 232 ASP cc_start: 0.8869 (m-30) cc_final: 0.8578 (m-30) REVERT: C 364 GLU cc_start: 0.9229 (tp30) cc_final: 0.8922 (tp30) REVERT: C 440 PHE cc_start: 0.9301 (t80) cc_final: 0.9000 (t80) REVERT: D 8 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8481 (mp10) REVERT: D 16 LYS cc_start: 0.9455 (OUTLIER) cc_final: 0.9104 (mtmp) REVERT: D 95 ASP cc_start: 0.9078 (OUTLIER) cc_final: 0.8555 (p0) REVERT: D 196 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8311 (mt-10) REVERT: D 259 ASN cc_start: 0.9131 (m-40) cc_final: 0.8910 (m-40) REVERT: E 113 ASP cc_start: 0.9476 (m-30) cc_final: 0.9138 (m-30) REVERT: E 155 ASP cc_start: 0.8824 (OUTLIER) cc_final: 0.8128 (t0) REVERT: E 176 ILE cc_start: 0.9257 (mm) cc_final: 0.8951 (mm) REVERT: E 232 ASP cc_start: 0.9002 (m-30) cc_final: 0.8754 (m-30) REVERT: E 481 GLN cc_start: 0.9281 (OUTLIER) cc_final: 0.8806 (tp-100) REVERT: E 489 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6879 (ptm) REVERT: F 129 ARG cc_start: 0.9160 (ptt-90) cc_final: 0.8808 (ptp90) REVERT: F 155 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8409 (t0) REVERT: F 166 GLU cc_start: 0.6668 (tm-30) cc_final: 0.6006 (tm-30) REVERT: F 251 SER cc_start: 0.8676 (t) cc_final: 0.8336 (p) REVERT: F 257 ILE cc_start: 0.9387 (OUTLIER) cc_final: 0.9143 (tp) REVERT: F 403 ASP cc_start: 0.8917 (t0) cc_final: 0.8577 (t0) REVERT: F 463 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8667 (mp) outliers start: 100 outliers final: 54 residues processed: 275 average time/residue: 0.2486 time to fit residues: 118.4993 Evaluate side-chains 250 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 185 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 226 CYS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 49 ILE Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 458 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 400 LEU Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 312 optimal weight: 40.0000 chunk 108 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 32 optimal weight: 5.9990 chunk 186 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 229 optimal weight: 9.9990 chunk 45 optimal weight: 0.9980 chunk 291 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 379 optimal weight: 50.0000 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.068054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.049305 restraints weight = 221300.742| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.31 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.123 48571 Z= 0.143 Angle : 0.482 11.646 70240 Z= 0.278 Chirality : 0.035 0.312 8517 Planarity : 0.004 0.063 5277 Dihedral : 23.707 179.203 18862 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.70 % Allowed : 19.15 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.16), residues: 2964 helix: 2.59 (0.13), residues: 1644 sheet: -1.69 (0.28), residues: 252 loop : 0.10 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 235 TYR 0.025 0.001 TYR E 381 PHE 0.035 0.001 PHE B 180 TRP 0.011 0.001 TRP C 250 HIS 0.010 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (48571) covalent geometry : angle 0.48244 / 0.28 (70240) hydrogen bonds : bond 0.06581 / 4.26 ( 2142) hydrogen bonds : angle 4.18605 / 2.99 ( 4948) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 203 time to evaluate : 1.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8452 (mt-10) REVERT: A 232 ASP cc_start: 0.9085 (t0) cc_final: 0.8765 (t0) REVERT: A 284 SER cc_start: 0.8968 (m) cc_final: 0.8747 (t) REVERT: B 31 LEU cc_start: 0.9733 (tp) cc_final: 0.9121 (tt) REVERT: B 155 ASP cc_start: 0.8954 (OUTLIER) cc_final: 0.8731 (t70) REVERT: B 161 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7471 (mtp180) REVERT: B 184 GLN cc_start: 0.8740 (mt0) cc_final: 0.8285 (tt0) REVERT: B 187 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8280 (mp0) REVERT: B 228 LYS cc_start: 0.9168 (tppt) cc_final: 0.8801 (tppt) REVERT: B 232 ASP cc_start: 0.8750 (m-30) cc_final: 0.8243 (m-30) REVERT: B 236 GLU cc_start: 0.9108 (tp30) cc_final: 0.8644 (tp30) REVERT: C 4 GLU cc_start: 0.9205 (tt0) cc_final: 0.8926 (tm-30) REVERT: C 187 GLU cc_start: 0.9226 (mm-30) cc_final: 0.8578 (mm-30) REVERT: C 232 ASP cc_start: 0.8877 (m-30) cc_final: 0.8563 (m-30) REVERT: C 364 GLU cc_start: 0.9251 (tp30) cc_final: 0.8932 (tp30) REVERT: C 440 PHE cc_start: 0.9297 (t80) cc_final: 0.9012 (t80) REVERT: D 8 GLN cc_start: 0.8797 (OUTLIER) cc_final: 0.8475 (mp10) REVERT: D 16 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9117 (mtmp) REVERT: D 95 ASP cc_start: 0.8982 (OUTLIER) cc_final: 0.8576 (p0) REVERT: D 196 GLU cc_start: 0.8871 (mt-10) cc_final: 0.8370 (mt-10) REVERT: E 113 ASP cc_start: 0.9493 (m-30) cc_final: 0.9231 (m-30) REVERT: E 155 ASP cc_start: 0.8838 (OUTLIER) cc_final: 0.8151 (t0) REVERT: E 232 ASP cc_start: 0.8999 (m-30) cc_final: 0.8789 (m-30) REVERT: E 392 LYS cc_start: 0.7424 (OUTLIER) cc_final: 0.6613 (ttpt) REVERT: E 481 GLN cc_start: 0.9269 (OUTLIER) cc_final: 0.8780 (tp-100) REVERT: E 489 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6951 (ptm) REVERT: F 129 ARG cc_start: 0.9162 (ptt-90) cc_final: 0.8849 (ptp90) REVERT: F 155 ASP cc_start: 0.8765 (OUTLIER) cc_final: 0.8385 (t0) REVERT: F 166 GLU cc_start: 0.6708 (tm-30) cc_final: 0.6033 (tm-30) REVERT: F 235 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8412 (mtp85) REVERT: F 251 SER cc_start: 0.8617 (t) cc_final: 0.8247 (p) REVERT: F 257 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9151 (tp) REVERT: F 403 ASP cc_start: 0.8894 (t0) cc_final: 0.8542 (t0) REVERT: F 463 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8674 (mp) outliers start: 100 outliers final: 57 residues processed: 279 average time/residue: 0.2488 time to fit residues: 119.3108 Evaluate side-chains 251 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 182 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 482 GLU Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 16 LYS Chi-restraints excluded: chain D residue 95 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 257 ILE Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 489 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 128 optimal weight: 0.6980 chunk 340 optimal weight: 70.0000 chunk 105 optimal weight: 7.9990 chunk 57 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 343 optimal weight: 50.0000 chunk 77 optimal weight: 6.9990 chunk 246 optimal weight: 6.9990 chunk 187 optimal weight: 4.9990 chunk 285 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 259 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.067450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.048036 restraints weight = 227575.993| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 3.36 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.107 48571 Z= 0.194 Angle : 0.513 11.969 70240 Z= 0.292 Chirality : 0.036 0.247 8517 Planarity : 0.004 0.058 5277 Dihedral : 23.708 179.425 18856 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 12.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.67 % Allowed : 19.56 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.16), residues: 2964 helix: 2.54 (0.13), residues: 1638 sheet: -1.71 (0.29), residues: 252 loop : 0.15 (0.21), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 35 TYR 0.021 0.001 TYR A 329 PHE 0.015 0.001 PHE F 92 TRP 0.011 0.001 TRP C 250 HIS 0.009 0.002 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00400 / 0.19 (48571) covalent geometry : angle 0.51349 / 0.29 (70240) hydrogen bonds : bond 0.06860 / 4.45 ( 2142) hydrogen bonds : angle 4.28133 / 3.05 ( 4948) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 186 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8689 (mt-10) cc_final: 0.8465 (mt-10) REVERT: A 232 ASP cc_start: 0.9119 (t0) cc_final: 0.8820 (t0) REVERT: A 284 SER cc_start: 0.8979 (m) cc_final: 0.8762 (t) REVERT: B 161 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7416 (mtp180) REVERT: B 184 GLN cc_start: 0.8686 (mt0) cc_final: 0.8378 (tt0) REVERT: B 187 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8265 (mp0) REVERT: B 228 LYS cc_start: 0.9210 (tppt) cc_final: 0.8816 (tppt) REVERT: B 232 ASP cc_start: 0.8762 (m-30) cc_final: 0.8256 (m-30) REVERT: B 236 GLU cc_start: 0.9166 (tp30) cc_final: 0.8629 (tp30) REVERT: C 4 GLU cc_start: 0.9226 (tt0) cc_final: 0.8927 (tm-30) REVERT: C 232 ASP cc_start: 0.8903 (m-30) cc_final: 0.8584 (m-30) REVERT: C 364 GLU cc_start: 0.9243 (tp30) cc_final: 0.8936 (tp30) REVERT: C 440 PHE cc_start: 0.9318 (t80) cc_final: 0.9049 (t80) REVERT: D 8 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8551 (mp10) REVERT: D 196 GLU cc_start: 0.8843 (mt-10) cc_final: 0.8313 (mt-10) REVERT: D 253 GLU cc_start: 0.8844 (mt-10) cc_final: 0.8430 (pm20) REVERT: D 448 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8481 (p0) REVERT: E 113 ASP cc_start: 0.9484 (m-30) cc_final: 0.9192 (m-30) REVERT: E 155 ASP cc_start: 0.8869 (t70) cc_final: 0.8218 (t0) REVERT: E 232 ASP cc_start: 0.9002 (m-30) cc_final: 0.8790 (m-30) REVERT: E 392 LYS cc_start: 0.7519 (OUTLIER) cc_final: 0.6744 (ttpt) REVERT: E 481 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8760 (tp-100) REVERT: F 129 ARG cc_start: 0.9171 (ptt-90) cc_final: 0.8899 (ptp90) REVERT: F 166 GLU cc_start: 0.6762 (tm-30) cc_final: 0.6101 (tm-30) REVERT: F 235 ARG cc_start: 0.8870 (mtp85) cc_final: 0.8611 (mtp85) REVERT: F 251 SER cc_start: 0.8617 (t) cc_final: 0.8230 (p) REVERT: F 403 ASP cc_start: 0.8975 (t0) cc_final: 0.8665 (t0) REVERT: F 448 ASP cc_start: 0.9276 (OUTLIER) cc_final: 0.8598 (p0) REVERT: F 463 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8727 (mp) outliers start: 99 outliers final: 70 residues processed: 265 average time/residue: 0.1884 time to fit residues: 86.6810 Evaluate side-chains 256 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 179 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 226 CYS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 410 LEU Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain E residue 481 GLN Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 84 optimal weight: 6.9990 chunk 94 optimal weight: 7.9990 chunk 339 optimal weight: 50.0000 chunk 324 optimal weight: 50.0000 chunk 88 optimal weight: 2.9990 chunk 383 optimal weight: 30.0000 chunk 112 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 385 optimal weight: 30.0000 chunk 214 optimal weight: 5.9990 chunk 286 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.067335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.047971 restraints weight = 227842.150| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 3.36 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 48571 Z= 0.180 Angle : 0.508 12.535 70240 Z= 0.289 Chirality : 0.036 0.284 8517 Planarity : 0.004 0.061 5277 Dihedral : 23.741 179.492 18853 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.26 % Allowed : 20.11 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.16), residues: 2964 helix: 2.52 (0.13), residues: 1638 sheet: -1.80 (0.29), residues: 240 loop : 0.05 (0.21), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 235 TYR 0.022 0.001 TYR A 329 PHE 0.013 0.001 PHE B 469 TRP 0.013 0.001 TRP C 250 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 (48571) covalent geometry : angle 0.50805 / 0.29 (70240) hydrogen bonds : bond 0.06766 / 4.38 ( 2142) hydrogen bonds : angle 4.27725 / 3.04 ( 4948) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 189 time to evaluate : 1.189 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8431 (mt-10) REVERT: A 232 ASP cc_start: 0.9175 (t70) cc_final: 0.8870 (t0) REVERT: A 235 ARG cc_start: 0.8249 (mtt180) cc_final: 0.7842 (mtt90) REVERT: A 284 SER cc_start: 0.8988 (m) cc_final: 0.8750 (t) REVERT: B 184 GLN cc_start: 0.8655 (mt0) cc_final: 0.8431 (tt0) REVERT: B 187 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8266 (mp0) REVERT: B 228 LYS cc_start: 0.9216 (tppt) cc_final: 0.8814 (tppt) REVERT: B 232 ASP cc_start: 0.8787 (m-30) cc_final: 0.8272 (m-30) REVERT: B 236 GLU cc_start: 0.9170 (tp30) cc_final: 0.8648 (tp30) REVERT: B 458 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8857 (pt) REVERT: C 4 GLU cc_start: 0.9232 (tt0) cc_final: 0.8932 (tm-30) REVERT: C 187 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8622 (mm-30) REVERT: C 232 ASP cc_start: 0.8920 (m-30) cc_final: 0.8579 (m-30) REVERT: C 364 GLU cc_start: 0.9253 (tp30) cc_final: 0.8962 (tp30) REVERT: C 440 PHE cc_start: 0.9369 (t80) cc_final: 0.9109 (t80) REVERT: D 8 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8574 (mp10) REVERT: D 183 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8856 (mm-30) REVERT: D 196 GLU cc_start: 0.8892 (mt-10) cc_final: 0.8351 (mt-10) REVERT: D 448 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8448 (p0) REVERT: E 113 ASP cc_start: 0.9492 (m-30) cc_final: 0.9194 (m-30) REVERT: E 155 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8274 (t0) REVERT: E 232 ASP cc_start: 0.9029 (m-30) cc_final: 0.8803 (m-30) REVERT: E 392 LYS cc_start: 0.7481 (OUTLIER) cc_final: 0.6732 (ttpt) REVERT: F 129 ARG cc_start: 0.9175 (ptt-90) cc_final: 0.8903 (ptp90) REVERT: F 155 ASP cc_start: 0.8762 (t70) cc_final: 0.8370 (t0) REVERT: F 166 GLU cc_start: 0.6756 (tm-30) cc_final: 0.6070 (tm-30) REVERT: F 251 SER cc_start: 0.8491 (t) cc_final: 0.8184 (p) REVERT: F 403 ASP cc_start: 0.8950 (t0) cc_final: 0.8657 (t0) REVERT: F 463 LEU cc_start: 0.8984 (OUTLIER) cc_final: 0.8434 (tp) outliers start: 88 outliers final: 67 residues processed: 258 average time/residue: 0.1924 time to fit residues: 86.9993 Evaluate side-chains 253 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 180 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 226 CYS Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 257 ILE Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 226 CYS Chi-restraints excluded: chain C residue 265 THR Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 11 ILE Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 116 ILE Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 42 optimal weight: 4.9990 chunk 331 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 27 optimal weight: 9.9990 chunk 226 optimal weight: 0.9990 chunk 170 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 214 optimal weight: 5.9990 chunk 366 optimal weight: 40.0000 chunk 342 optimal weight: 30.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 262 ASN ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 159 ASN F 223 ASN F 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.067142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.048076 restraints weight = 224354.318| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 3.35 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.3447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 48571 Z= 0.167 Angle : 0.499 12.791 70240 Z= 0.285 Chirality : 0.036 0.307 8517 Planarity : 0.004 0.060 5277 Dihedral : 23.729 179.269 18853 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.33 % Allowed : 20.30 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.16), residues: 2964 helix: 2.57 (0.13), residues: 1632 sheet: -1.65 (0.29), residues: 252 loop : 0.15 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 39 TYR 0.022 0.001 TYR A 329 PHE 0.012 0.001 PHE F 92 TRP 0.016 0.001 TRP C 250 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (48571) covalent geometry : angle 0.49895 / 0.28 (70240) hydrogen bonds : bond 0.06724 / 4.35 ( 2142) hydrogen bonds : angle 4.25157 / 3.02 ( 4948) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 185 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8406 (mt-10) REVERT: A 230 ASP cc_start: 0.8987 (t0) cc_final: 0.8757 (t0) REVERT: A 232 ASP cc_start: 0.9180 (t70) cc_final: 0.8863 (t0) REVERT: A 284 SER cc_start: 0.8962 (m) cc_final: 0.8756 (t) REVERT: B 161 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.7498 (mtp180) REVERT: B 187 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8417 (mp0) REVERT: B 228 LYS cc_start: 0.9211 (tppt) cc_final: 0.8817 (tppt) REVERT: B 232 ASP cc_start: 0.8751 (m-30) cc_final: 0.8244 (m-30) REVERT: B 236 GLU cc_start: 0.9168 (tp30) cc_final: 0.8654 (tp30) REVERT: B 458 ILE cc_start: 0.9102 (OUTLIER) cc_final: 0.8878 (pt) REVERT: C 4 GLU cc_start: 0.9220 (tt0) cc_final: 0.8965 (tm-30) REVERT: C 12 LEU cc_start: 0.9618 (OUTLIER) cc_final: 0.9416 (mt) REVERT: C 187 GLU cc_start: 0.9197 (mm-30) cc_final: 0.8558 (mm-30) REVERT: C 232 ASP cc_start: 0.8920 (m-30) cc_final: 0.8578 (m-30) REVERT: C 259 ASN cc_start: 0.9122 (m-40) cc_final: 0.8848 (m110) REVERT: C 364 GLU cc_start: 0.9249 (tp30) cc_final: 0.8967 (tp30) REVERT: D 8 GLN cc_start: 0.8871 (OUTLIER) cc_final: 0.8556 (mp10) REVERT: D 196 GLU cc_start: 0.8905 (mt-10) cc_final: 0.8466 (mt-10) REVERT: D 253 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8432 (pm20) REVERT: D 448 ASP cc_start: 0.9075 (OUTLIER) cc_final: 0.8462 (p0) REVERT: E 113 ASP cc_start: 0.9472 (m-30) cc_final: 0.9166 (m-30) REVERT: E 155 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.8191 (t0) REVERT: E 392 LYS cc_start: 0.7495 (OUTLIER) cc_final: 0.6742 (ttpt) REVERT: F 129 ARG cc_start: 0.9175 (ptt-90) cc_final: 0.8918 (ptp90) REVERT: F 155 ASP cc_start: 0.8719 (t70) cc_final: 0.8374 (t0) REVERT: F 166 GLU cc_start: 0.6810 (tm-30) cc_final: 0.6125 (tm-30) REVERT: F 235 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8485 (mtp85) REVERT: F 251 SER cc_start: 0.8487 (t) cc_final: 0.8204 (p) REVERT: F 403 ASP cc_start: 0.8931 (t0) cc_final: 0.8649 (t0) REVERT: F 448 ASP cc_start: 0.9253 (OUTLIER) cc_final: 0.8602 (p0) REVERT: F 463 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8431 (tp) outliers start: 90 outliers final: 67 residues processed: 255 average time/residue: 0.1861 time to fit residues: 82.0743 Evaluate side-chains 249 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 173 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ILE Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 72 SER Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 304 LEU Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 100 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain C residue 11 ILE Chi-restraints excluded: chain C residue 12 LEU Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 226 CYS Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 310 VAL Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 218 SER Chi-restraints excluded: chain E residue 291 LEU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 263 ILE Chi-restraints excluded: chain F residue 273 ILE Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 84 optimal weight: 10.0000 chunk 257 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 146 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 327 optimal weight: 40.0000 chunk 88 optimal weight: 3.9990 chunk 236 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 351 optimal weight: 40.0000 chunk 263 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 146 HIS ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.067655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.048985 restraints weight = 222285.113| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 3.34 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 48571 Z= 0.129 Angle : 0.478 12.782 70240 Z= 0.274 Chirality : 0.035 0.290 8517 Planarity : 0.004 0.061 5277 Dihedral : 23.689 179.806 18853 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.59 % Allowed : 21.19 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.16), residues: 2964 helix: 2.61 (0.13), residues: 1644 sheet: -1.63 (0.30), residues: 240 loop : 0.01 (0.21), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 235 TYR 0.026 0.001 TYR C 329 PHE 0.010 0.001 PHE C 397 TRP 0.015 0.001 TRP C 250 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.13 (48571) covalent geometry : angle 0.47762 / 0.27 (70240) hydrogen bonds : bond 0.06456 / 4.15 ( 2142) hydrogen bonds : angle 4.16694 / 2.96 ( 4948) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 196 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8650 (mt-10) cc_final: 0.8383 (mt-10) REVERT: A 228 LYS cc_start: 0.9391 (tppt) cc_final: 0.9027 (tppt) REVERT: A 230 ASP cc_start: 0.8946 (t0) cc_final: 0.8676 (t0) REVERT: A 232 ASP cc_start: 0.9174 (t70) cc_final: 0.8857 (t0) REVERT: A 235 ARG cc_start: 0.8137 (mtt180) cc_final: 0.7833 (mtt180) REVERT: A 284 SER cc_start: 0.8980 (m) cc_final: 0.8777 (t) REVERT: B 161 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.7510 (mtp180) REVERT: B 187 GLU cc_start: 0.8737 (mm-30) cc_final: 0.8180 (mp0) REVERT: B 228 LYS cc_start: 0.9198 (tppt) cc_final: 0.8827 (tppt) REVERT: B 232 ASP cc_start: 0.8763 (m-30) cc_final: 0.8277 (m-30) REVERT: B 236 GLU cc_start: 0.9152 (tp30) cc_final: 0.8634 (tp30) REVERT: B 458 ILE cc_start: 0.9112 (OUTLIER) cc_final: 0.8897 (pt) REVERT: C 4 GLU cc_start: 0.9207 (tt0) cc_final: 0.8947 (tm-30) REVERT: C 155 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8560 (t0) REVERT: C 187 GLU cc_start: 0.9187 (mm-30) cc_final: 0.8547 (mm-30) REVERT: C 232 ASP cc_start: 0.8908 (m-30) cc_final: 0.8584 (m-30) REVERT: C 259 ASN cc_start: 0.9112 (m-40) cc_final: 0.8718 (m110) REVERT: C 364 GLU cc_start: 0.9249 (tp30) cc_final: 0.8971 (tp30) REVERT: D 8 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8555 (mp10) REVERT: D 196 GLU cc_start: 0.8915 (mt-10) cc_final: 0.8439 (mt-10) REVERT: D 253 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8502 (pm20) REVERT: D 281 GLU cc_start: 0.8920 (tp30) cc_final: 0.8672 (tp30) REVERT: D 448 ASP cc_start: 0.9077 (OUTLIER) cc_final: 0.8449 (p0) REVERT: E 155 ASP cc_start: 0.8832 (OUTLIER) cc_final: 0.8167 (t0) REVERT: E 392 LYS cc_start: 0.7458 (OUTLIER) cc_final: 0.6759 (ttpt) REVERT: F 129 ARG cc_start: 0.9192 (ptt-90) cc_final: 0.8940 (ptp90) REVERT: F 155 ASP cc_start: 0.8805 (OUTLIER) cc_final: 0.8386 (t0) REVERT: F 166 GLU cc_start: 0.6796 (tm-30) cc_final: 0.6118 (tm-30) REVERT: F 235 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8464 (mtp85) REVERT: F 251 SER cc_start: 0.8460 (t) cc_final: 0.8218 (p) REVERT: F 403 ASP cc_start: 0.8887 (t0) cc_final: 0.8589 (t0) REVERT: F 448 ASP cc_start: 0.9249 (OUTLIER) cc_final: 0.8643 (p0) REVERT: F 463 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8435 (tp) outliers start: 70 outliers final: 50 residues processed: 251 average time/residue: 0.1839 time to fit residues: 79.5032 Evaluate side-chains 244 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 184 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ASP Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 111 ILE Chi-restraints excluded: chain A residue 215 THR Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 449 ILE Chi-restraints excluded: chain A residue 468 SER Chi-restraints excluded: chain B residue 21 ASP Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 199 ILE Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 248 ILE Chi-restraints excluded: chain B residue 264 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain C residue 155 ASP Chi-restraints excluded: chain C residue 218 SER Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 284 SER Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 203 PHE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 395 MET Chi-restraints excluded: chain D residue 448 ASP Chi-restraints excluded: chain D residue 468 SER Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 488 ILE Chi-restraints excluded: chain E residue 1 MET Chi-restraints excluded: chain E residue 29 VAL Chi-restraints excluded: chain E residue 155 ASP Chi-restraints excluded: chain E residue 166 GLU Chi-restraints excluded: chain E residue 304 LEU Chi-restraints excluded: chain E residue 320 VAL Chi-restraints excluded: chain E residue 392 LYS Chi-restraints excluded: chain E residue 410 LEU Chi-restraints excluded: chain E residue 450 VAL Chi-restraints excluded: chain F residue 100 ASP Chi-restraints excluded: chain F residue 155 ASP Chi-restraints excluded: chain F residue 162 THR Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 450 VAL Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 471 LEU Chi-restraints excluded: chain F residue 489 MET Chi-restraints excluded: chain F residue 490 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 32 optimal weight: 5.9990 chunk 322 optimal weight: 50.0000 chunk 214 optimal weight: 5.9990 chunk 135 optimal weight: 0.9980 chunk 283 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 308 optimal weight: 50.0000 chunk 263 optimal weight: 3.9990 chunk 180 optimal weight: 6.9990 chunk 329 optimal weight: 50.0000 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.067529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.048274 restraints weight = 226916.484| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 3.37 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 48571 Z= 0.159 Angle : 0.493 12.596 70240 Z= 0.281 Chirality : 0.035 0.279 8517 Planarity : 0.004 0.057 5277 Dihedral : 23.670 179.315 18853 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.67 % Allowed : 21.30 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.01 (0.16), residues: 2964 helix: 2.59 (0.13), residues: 1638 sheet: -1.53 (0.30), residues: 252 loop : 0.12 (0.21), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 235 TYR 0.023 0.001 TYR C 329 PHE 0.020 0.001 PHE F 92 TRP 0.013 0.001 TRP C 250 HIS 0.009 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.16 (48571) covalent geometry : angle 0.49326 / 0.28 (70240) hydrogen bonds : bond 0.06625 / 4.26 ( 2142) hydrogen bonds : angle 4.20492 / 2.99 ( 4948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6172.41 seconds wall clock time: 108 minutes 1.41 seconds (6481.41 seconds total)