Starting phenix.real_space_refine on Mon Aug 10 10:12:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vma_65181/08_2026/9vma_65181_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vma_65181/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9vma_65181/08_2026/9vma_65181_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vma_65181/08_2026/9vma_65181_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vma_65181/08_2026/9vma_65181.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vma_65181/08_2026/9vma_65181.map" } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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: 9.68, per 1000 atoms: 0.21 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: 3.63 Conformation dependent library (CDL) restraints added in 1.2 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: 6.38 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: 10.13 Time building geometry restraints manager: 4.98 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: 68853 2.71 - 5.42: 1105 5.42 - 8.12: 265 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: 8085 0.137 - 0.275: 227 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: 1.700 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: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.110 Process input model: 43.830 Find NCS groups from input model: 1.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.910 ------------------------------------------------------------------------------- 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= 0.383 Angle : 0.876 13.539 70240 Z= 0.579 Chirality : 0.094 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 0.00573 / 0.38 (48571) covalent geometry : angle 0.87646 / 0.58 (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 : 0.851 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: A 218 SER cc_start: 0.9101 (OUTLIER) cc_final: 0.8487 (m) REVERT: A 392 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7895 (ptmm) 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: 0.9061 (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: 0.8132 (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: 0.6557 (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: 0.2644 time to fit residues: 233.3260 Evaluate side-chains 240 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 220 time to evaluate : 1.214 ------------------------------------------------------------------------------- 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: 4.9990 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 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: 3.9588 ------------------------------------------------------------------------------- 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 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 ASN C 490 ASN D 150 GLN D 252 GLN D 259 ASN 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: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.069564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.050855 restraints weight = 221061.499| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.33 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 48571 Z= 0.182 Angle : 0.589 9.756 70240 Z= 0.329 Chirality : 0.042 0.396 8517 Planarity : 0.004 0.044 5277 Dihedral : 23.872 179.118 18886 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.70 % Allowed : 17.59 % 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: 1.80 (0.16), residues: 2964 helix: 2.44 (0.13), residues: 1596 sheet: -1.80 (0.32), residues: 216 loop : 0.07 (0.20), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 205 TYR 0.025 0.002 TYR B 329 PHE 0.019 0.002 PHE C 303 TRP 0.011 0.001 TRP C 227 HIS 0.010 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (48571) covalent geometry : angle 0.58922 / 0.33 (70240) hydrogen bonds : bond 0.08860 / 5.72 ( 2142) hydrogen bonds : angle 4.74323 / 3.41 ( 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 340 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 240 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8680 (mt) REVERT: A 196 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8516 (mt-10) REVERT: A 232 ASP cc_start: 0.8969 (t70) cc_final: 0.8667 (t70) REVERT: A 284 SER cc_start: 0.9033 (OUTLIER) cc_final: 0.8777 (t) REVERT: A 392 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7725 (ptmm) REVERT: B 187 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8180 (mm-30) REVERT: B 232 ASP cc_start: 0.8736 (m-30) cc_final: 0.8320 (m-30) REVERT: B 267 PHE cc_start: 0.8826 (t80) cc_final: 0.8593 (t80) REVERT: C 1 MET cc_start: 0.8448 (tmm) cc_final: 0.8042 (tmm) REVERT: C 144 ASN cc_start: 0.8161 (OUTLIER) cc_final: 0.7894 (p0) REVERT: C 228 LYS cc_start: 0.9149 (tppp) cc_final: 0.8669 (tppt) REVERT: C 232 ASP cc_start: 0.8882 (m-30) cc_final: 0.8648 (m-30) REVERT: C 364 GLU cc_start: 0.9226 (tp30) cc_final: 0.9002 (tp30) REVERT: D 8 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8351 (mp10) REVERT: D 16 LYS cc_start: 0.9427 (OUTLIER) cc_final: 0.9159 (mttp) REVERT: D 156 LEU cc_start: 0.9760 (mt) cc_final: 0.9510 (mp) REVERT: D 196 GLU cc_start: 0.8848 (mt-10) cc_final: 0.8423 (mt-10) REVERT: D 477 GLN cc_start: 0.8336 (mm110) cc_final: 0.8042 (mm110) REVERT: E 155 ASP cc_start: 0.8801 (OUTLIER) cc_final: 0.7993 (t0) REVERT: E 167 PHE cc_start: 0.8513 (m-80) cc_final: 0.8083 (m-80) REVERT: E 231 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8232 (tm-30) REVERT: E 251 SER cc_start: 0.9127 (t) cc_final: 0.8808 (p) REVERT: E 252 GLN cc_start: 0.8967 (OUTLIER) cc_final: 0.8691 (mm-40) REVERT: F 155 ASP cc_start: 0.8674 (OUTLIER) cc_final: 0.8252 (t0) REVERT: F 166 GLU cc_start: 0.6336 (tm-30) cc_final: 0.5706 (tm-30) REVERT: F 235 ARG cc_start: 0.8954 (mtp85) cc_final: 0.8657 (mtp85) REVERT: F 279 LYS cc_start: 0.8406 (mtpt) cc_final: 0.8157 (mtmt) REVERT: F 403 ASP cc_start: 0.8807 (t0) cc_final: 0.8468 (t0) outliers start: 100 outliers final: 40 residues processed: 318 average time/residue: 0.2392 time to fit residues: 130.9688 Evaluate side-chains 243 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 193 time to evaluate : 1.169 ------------------------------------------------------------------------------- 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 183 GLU 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 226 CYS 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 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: 40.0000 chunk 192 optimal weight: 9.9990 chunk 383 optimal weight: 50.0000 chunk 113 optimal weight: 5.9990 chunk 165 optimal weight: 0.0050 chunk 147 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 224 optimal weight: 3.9990 chunk 328 optimal weight: 50.0000 chunk 105 optimal weight: 4.9990 overall best weight: 4.0002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 231 GLN ** 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 5 GLN D 259 ASN E 252 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.069020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.049707 restraints weight = 222934.981| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.33 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 48571 Z= 0.163 Angle : 0.532 10.203 70240 Z= 0.299 Chirality : 0.039 0.370 8517 Planarity : 0.004 0.043 5277 Dihedral : 23.786 178.053 18873 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 3.74 % Allowed : 17.74 % Favored : 78.52 % 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: 1.79 (0.16), residues: 2964 helix: 2.47 (0.13), residues: 1596 sheet: -1.84 (0.29), residues: 252 loop : 0.10 (0.20), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG F 388 TYR 0.025 0.002 TYR E 381 PHE 0.022 0.001 PHE A 391 TRP 0.010 0.001 TRP C 250 HIS 0.009 0.001 HIS F 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (48571) covalent geometry : angle 0.53163 / 0.30 (70240) hydrogen bonds : bond 0.07747 / 5.01 ( 2142) hydrogen bonds : angle 4.47462 / 3.20 ( 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 321 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 220 time to evaluate : 0.783 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8428 (mt-10) REVERT: A 196 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8494 (mt-10) REVERT: A 232 ASP cc_start: 0.8985 (t70) cc_final: 0.8617 (t0) REVERT: A 235 ARG cc_start: 0.8251 (mtt180) cc_final: 0.8006 (mtt180) REVERT: A 284 SER cc_start: 0.9021 (OUTLIER) cc_final: 0.8768 (t) REVERT: A 289 LYS cc_start: 0.9262 (tppt) cc_final: 0.8977 (mmmt) REVERT: A 392 LYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7600 (ptmm) REVERT: B 187 GLU cc_start: 0.8681 (mm-30) cc_final: 0.8297 (mp0) REVERT: B 228 LYS cc_start: 0.9122 (tppt) cc_final: 0.8736 (tppt) REVERT: B 232 ASP cc_start: 0.8781 (m-30) cc_final: 0.8290 (m-30) REVERT: B 267 PHE cc_start: 0.8873 (t80) cc_final: 0.8603 (t80) REVERT: C 1 MET cc_start: 0.8234 (tmm) cc_final: 0.7425 (tmm) REVERT: C 232 ASP cc_start: 0.8889 (m-30) cc_final: 0.8478 (m-30) REVERT: D 8 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8443 (mp10) REVERT: D 16 LYS cc_start: 0.9452 (OUTLIER) cc_final: 0.9135 (mttp) REVERT: D 95 ASP cc_start: 0.9062 (OUTLIER) cc_final: 0.8586 (p0) REVERT: D 151 ASP cc_start: 0.9504 (t0) cc_final: 0.8813 (t0) REVERT: D 156 LEU cc_start: 0.9749 (mt) cc_final: 0.9539 (mp) REVERT: D 181 LEU cc_start: 0.9166 (OUTLIER) cc_final: 0.8902 (tp) REVERT: D 196 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8302 (mt-10) REVERT: D 239 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.7739 (tptt) REVERT: E 113 ASP cc_start: 0.9468 (m-30) cc_final: 0.9091 (m-30) REVERT: E 155 ASP cc_start: 0.8830 (t70) cc_final: 0.8096 (t0) REVERT: E 232 ASP cc_start: 0.8972 (m-30) cc_final: 0.8727 (m-30) REVERT: F 155 ASP cc_start: 0.8738 (OUTLIER) cc_final: 0.8355 (t0) REVERT: F 166 GLU cc_start: 0.6583 (tm-30) cc_final: 0.5977 (tm-30) REVERT: F 235 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8670 (mtp85) REVERT: F 403 ASP cc_start: 0.8838 (t0) cc_final: 0.8465 (t0) REVERT: F 482 GLU cc_start: 0.9082 (OUTLIER) cc_final: 0.8727 (mp0) outliers start: 101 outliers final: 50 residues processed: 299 average time/residue: 0.2160 time to fit residues: 112.9988 Evaluate side-chains 241 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 182 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 373 LEU Chi-restraints excluded: chain A residue 392 LYS Chi-restraints excluded: chain B residue 21 ASP 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 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 218 SER Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 239 LYS 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 233 LEU Chi-restraints excluded: chain E residue 238 VAL Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 273 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 289 LYS 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: 50.0000 chunk 87 optimal weight: 9.9990 chunk 363 optimal weight: 50.0000 chunk 80 optimal weight: 3.9990 chunk 270 optimal weight: 0.6980 chunk 112 optimal weight: 3.9990 chunk 377 optimal weight: 50.0000 chunk 212 optimal weight: 5.9990 chunk 239 optimal weight: 5.9990 chunk 223 optimal weight: 6.9990 chunk 287 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- 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 262 ASN E 231 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 = 0.3642 r_free = 0.3642 target = 0.068554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.049704 restraints weight = 220776.044| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.34 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 48571 Z= 0.145 Angle : 0.506 11.256 70240 Z= 0.285 Chirality : 0.038 0.371 8517 Planarity : 0.004 0.056 5277 Dihedral : 23.740 178.376 18870 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.81 % Allowed : 18.78 % Favored : 77.41 % 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: 1.89 (0.16), residues: 2964 helix: 2.47 (0.13), residues: 1650 sheet: -1.79 (0.29), residues: 252 loop : 0.14 (0.21), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 446 TYR 0.025 0.001 TYR E 381 PHE 0.027 0.001 PHE B 180 TRP 0.012 0.001 TRP C 413 HIS 0.010 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (48571) covalent geometry : angle 0.50584 / 0.28 (70240) hydrogen bonds : bond 0.07100 / 4.58 ( 2142) hydrogen bonds : angle 4.32189 / 3.10 ( 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 320 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 217 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8983 (OUTLIER) cc_final: 0.8652 (mt) REVERT: A 196 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8513 (mt-10) REVERT: A 232 ASP cc_start: 0.9037 (t0) cc_final: 0.8714 (t0) REVERT: A 263 ILE cc_start: 0.9416 (mm) cc_final: 0.9165 (mt) REVERT: A 284 SER cc_start: 0.8990 (OUTLIER) cc_final: 0.8710 (t) REVERT: A 289 LYS cc_start: 0.9271 (tppt) cc_final: 0.8974 (mmmt) REVERT: A 392 LYS cc_start: 0.7740 (OUTLIER) cc_final: 0.7413 (ptmm) REVERT: B 155 ASP cc_start: 0.8939 (OUTLIER) cc_final: 0.8727 (t70) REVERT: B 184 GLN cc_start: 0.8602 (mt0) cc_final: 0.8142 (tt0) REVERT: B 187 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8168 (mp0) REVERT: B 228 LYS cc_start: 0.9178 (tppt) cc_final: 0.8788 (tppt) REVERT: B 232 ASP cc_start: 0.8793 (m-30) cc_final: 0.8273 (m-30) REVERT: B 236 GLU cc_start: 0.9085 (tp30) cc_final: 0.8503 (tp30) REVERT: B 267 PHE cc_start: 0.8854 (t80) cc_final: 0.8621 (t80) REVERT: B 458 ILE cc_start: 0.9129 (OUTLIER) cc_final: 0.8908 (pt) REVERT: C 1 MET cc_start: 0.8282 (tmm) cc_final: 0.7644 (tmm) REVERT: C 232 ASP cc_start: 0.8846 (m-30) cc_final: 0.8587 (m-30) REVERT: C 440 PHE cc_start: 0.9316 (t80) cc_final: 0.8998 (t80) REVERT: D 8 GLN cc_start: 0.8771 (OUTLIER) cc_final: 0.8463 (mp10) REVERT: D 16 LYS cc_start: 0.9465 (OUTLIER) cc_final: 0.9076 (mtmp) REVERT: D 95 ASP cc_start: 0.8973 (OUTLIER) cc_final: 0.8486 (p0) REVERT: D 151 ASP cc_start: 0.9507 (t0) cc_final: 0.8743 (t0) REVERT: D 196 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8300 (mt-10) REVERT: D 239 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.7700 (tptt) REVERT: D 259 ASN cc_start: 0.9109 (m-40) cc_final: 0.8834 (m-40) REVERT: E 113 ASP cc_start: 0.9492 (m-30) cc_final: 0.9180 (m-30) REVERT: E 155 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8150 (t0) REVERT: E 232 ASP cc_start: 0.8999 (m-30) cc_final: 0.8769 (m-30) REVERT: E 236 GLU cc_start: 0.9000 (tp30) cc_final: 0.8791 (tp30) REVERT: E 481 GLN cc_start: 0.9294 (OUTLIER) cc_final: 0.8763 (tp-100) REVERT: F 129 ARG cc_start: 0.9168 (ptt-90) cc_final: 0.8936 (ptt180) REVERT: F 166 GLU cc_start: 0.6594 (tm-30) cc_final: 0.5955 (tm-30) REVERT: F 235 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8687 (mtp85) REVERT: F 257 ILE cc_start: 0.9407 (OUTLIER) cc_final: 0.8954 (tp) REVERT: F 403 ASP cc_start: 0.8848 (t0) cc_final: 0.8465 (t0) REVERT: F 482 GLU cc_start: 0.9092 (OUTLIER) cc_final: 0.8725 (mp0) outliers start: 103 outliers final: 53 residues processed: 299 average time/residue: 0.2512 time to fit residues: 131.4048 Evaluate side-chains 254 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 188 time to evaluate : 0.874 ------------------------------------------------------------------------------- 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 40 LEU 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 264 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 100 ASP 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 284 SER 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 270 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 211 ILE Chi-restraints excluded: chain D residue 218 SER Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 239 LYS 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 155 ASP 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 273 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 481 GLN Chi-restraints excluded: chain E residue 489 MET 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 36 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 305 optimal weight: 40.0000 chunk 188 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 26 optimal weight: 5.9990 chunk 206 optimal weight: 0.5980 chunk 367 optimal weight: 50.0000 chunk 12 optimal weight: 8.9990 chunk 151 optimal weight: 0.6980 chunk 196 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- 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 262 ASN 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 = 0.3642 r_free = 0.3642 target = 0.068454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049666 restraints weight = 220296.636| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.30 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 48571 Z= 0.135 Angle : 0.495 11.147 70240 Z= 0.277 Chirality : 0.037 0.369 8517 Planarity : 0.004 0.040 5277 Dihedral : 23.676 178.534 18863 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 3.74 % Allowed : 18.37 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.93 (0.16), residues: 2964 helix: 2.53 (0.13), residues: 1644 sheet: -1.71 (0.29), 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 0.026 0.001 TYR E 381 PHE 0.017 0.001 PHE F 92 TRP 0.012 0.001 TRP C 413 HIS 0.008 0.001 HIS B 178 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (48571) covalent geometry : angle 0.49486 / 0.28 (70240) hydrogen bonds : bond 0.06796 / 4.38 ( 2142) hydrogen bonds : angle 4.21739 / 3.01 ( 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 309 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 208 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8563 (mt) REVERT: A 196 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8478 (mt-10) REVERT: A 232 ASP cc_start: 0.9063 (t0) cc_final: 0.8766 (t0) REVERT: A 284 SER cc_start: 0.9025 (m) cc_final: 0.8761 (t) REVERT: A 289 LYS cc_start: 0.9245 (tppt) cc_final: 0.8954 (mmmt) REVERT: B 184 GLN cc_start: 0.8537 (mt0) cc_final: 0.8292 (tt0) REVERT: B 187 GLU cc_start: 0.8763 (mm-30) cc_final: 0.8241 (mp0) REVERT: B 228 LYS cc_start: 0.9180 (tppt) cc_final: 0.8802 (tppt) REVERT: B 232 ASP cc_start: 0.8778 (m-30) cc_final: 0.8271 (m-30) REVERT: B 236 GLU cc_start: 0.9095 (tp30) cc_final: 0.8632 (tp30) REVERT: B 267 PHE cc_start: 0.8878 (t80) cc_final: 0.8661 (t80) REVERT: B 458 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8909 (pt) REVERT: C 1 MET cc_start: 0.8271 (tmm) cc_final: 0.8049 (tmm) REVERT: C 232 ASP cc_start: 0.8861 (m-30) cc_final: 0.8575 (m-30) REVERT: C 440 PHE cc_start: 0.9282 (t80) cc_final: 0.8989 (t80) REVERT: D 8 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.8459 (mp10) REVERT: D 16 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.9119 (mtmp) REVERT: D 95 ASP cc_start: 0.9063 (OUTLIER) cc_final: 0.8656 (p0) REVERT: D 151 ASP cc_start: 0.9539 (t0) cc_final: 0.8887 (t0) REVERT: D 196 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8370 (mt-10) REVERT: D 205 ARG cc_start: 0.8097 (mtp180) cc_final: 0.7569 (mmm160) REVERT: D 239 LYS cc_start: 0.8640 (OUTLIER) cc_final: 0.7720 (tptt) REVERT: E 105 LYS cc_start: 0.8930 (mmmt) cc_final: 0.8726 (tppt) REVERT: E 113 ASP cc_start: 0.9482 (m-30) cc_final: 0.9181 (m-30) REVERT: E 155 ASP cc_start: 0.8836 (OUTLIER) cc_final: 0.8124 (t0) REVERT: E 232 ASP cc_start: 0.8998 (m-30) cc_final: 0.8775 (m-30) REVERT: E 251 SER cc_start: 0.9088 (p) cc_final: 0.8845 (p) REVERT: E 252 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8806 (mm-40) REVERT: E 481 GLN cc_start: 0.9280 (OUTLIER) cc_final: 0.8780 (tp-100) REVERT: E 489 MET cc_start: 0.7360 (OUTLIER) cc_final: 0.6834 (ptm) REVERT: F 129 ARG cc_start: 0.9177 (ptt-90) cc_final: 0.8822 (ptp90) REVERT: F 155 ASP cc_start: 0.8767 (OUTLIER) cc_final: 0.8368 (t0) REVERT: F 166 GLU cc_start: 0.6663 (tm-30) cc_final: 0.5997 (tm-30) REVERT: F 235 ARG cc_start: 0.8848 (mtp85) cc_final: 0.8594 (mtp85) REVERT: F 251 SER cc_start: 0.8710 (t) cc_final: 0.8299 (p) REVERT: F 257 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9147 (tp) REVERT: F 403 ASP cc_start: 0.8877 (t0) cc_final: 0.8515 (t0) REVERT: F 463 LEU cc_start: 0.8932 (OUTLIER) cc_final: 0.8666 (mp) outliers start: 101 outliers final: 56 residues processed: 287 average time/residue: 0.2442 time to fit residues: 122.5243 Evaluate side-chains 254 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 185 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 40 LEU 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 247 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 264 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 449 ILE 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 264 ILE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 284 SER 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 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 95 ASP Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 145 VAL 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 239 LYS Chi-restraints excluded: chain D residue 365 ILE Chi-restraints excluded: chain D residue 395 MET 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 248 ILE Chi-restraints excluded: chain E residue 252 GLN 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 481 GLN Chi-restraints excluded: chain E residue 489 MET Chi-restraints excluded: chain F residue 29 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 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: 50.0000 chunk 108 optimal weight: 9.9990 chunk 223 optimal weight: 20.0000 chunk 32 optimal weight: 6.9990 chunk 186 optimal weight: 0.0870 chunk 149 optimal weight: 5.9990 chunk 229 optimal weight: 10.0000 chunk 45 optimal weight: 7.9990 chunk 291 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 379 optimal weight: 50.0000 overall best weight: 3.0162 ------------------------------------------------------------------------------- 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 262 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.068388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049595 restraints weight = 220638.477| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 3.32 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 48571 Z= 0.133 Angle : 0.487 11.774 70240 Z= 0.272 Chirality : 0.036 0.367 8517 Planarity : 0.003 0.038 5277 Dihedral : 23.638 178.855 18858 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.37 % Allowed : 19.19 % Favored : 77.44 % 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: 2.04 (0.16), residues: 2964 helix: 2.62 (0.13), residues: 1644 sheet: -1.64 (0.29), residues: 252 loop : 0.14 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 39 TYR 0.024 0.001 TYR E 381 PHE 0.029 0.001 PHE B 180 TRP 0.011 0.001 TRP C 250 HIS 0.008 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.13 (48571) covalent geometry : angle 0.48738 / 0.27 (70240) hydrogen bonds : bond 0.06658 / 4.30 ( 2142) hydrogen bonds : angle 4.18009 / 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 293 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 202 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8716 (mt-10) cc_final: 0.8469 (mt-10) REVERT: A 232 ASP cc_start: 0.9097 (t0) cc_final: 0.8768 (t0) REVERT: A 284 SER cc_start: 0.9026 (m) cc_final: 0.8782 (t) REVERT: B 155 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8726 (t70) REVERT: B 161 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7444 (mtp180) REVERT: B 184 GLN cc_start: 0.8530 (mt0) cc_final: 0.8242 (tt0) REVERT: B 187 GLU cc_start: 0.8774 (mm-30) cc_final: 0.8253 (mp0) REVERT: B 228 LYS cc_start: 0.9183 (tppt) cc_final: 0.8812 (tppt) REVERT: B 232 ASP cc_start: 0.8794 (m-30) cc_final: 0.8312 (m-30) REVERT: B 236 GLU cc_start: 0.9125 (tp30) cc_final: 0.8577 (tp30) REVERT: B 267 PHE cc_start: 0.8798 (t80) cc_final: 0.8551 (t80) REVERT: B 395 MET cc_start: 0.9012 (tpp) cc_final: 0.8732 (tpp) REVERT: B 458 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8902 (pt) REVERT: C 1 MET cc_start: 0.8306 (tmm) cc_final: 0.7853 (tmm) REVERT: C 187 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8527 (mm-30) REVERT: C 232 ASP cc_start: 0.8867 (m-30) cc_final: 0.8574 (m-30) REVERT: C 440 PHE cc_start: 0.9302 (t80) cc_final: 0.9024 (t80) REVERT: C 482 GLU cc_start: 0.9062 (mt-10) cc_final: 0.8801 (tt0) REVERT: D 8 GLN cc_start: 0.8804 (OUTLIER) cc_final: 0.8515 (mp10) REVERT: D 16 LYS cc_start: 0.9441 (OUTLIER) cc_final: 0.9114 (mtmp) REVERT: D 95 ASP cc_start: 0.9080 (OUTLIER) cc_final: 0.8676 (p0) REVERT: D 151 ASP cc_start: 0.9550 (t0) cc_final: 0.8830 (t0) REVERT: D 183 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8739 (mm-30) REVERT: D 196 GLU cc_start: 0.8881 (mt-10) cc_final: 0.8375 (mt-10) REVERT: D 239 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.7748 (tptt) REVERT: E 113 ASP cc_start: 0.9476 (m-30) cc_final: 0.9219 (m-30) REVERT: E 155 ASP cc_start: 0.8843 (OUTLIER) cc_final: 0.8129 (t0) REVERT: E 232 ASP cc_start: 0.9001 (m-30) cc_final: 0.8788 (m-30) REVERT: E 392 LYS cc_start: 0.7394 (OUTLIER) cc_final: 0.6762 (ptpt) REVERT: E 481 GLN cc_start: 0.9273 (OUTLIER) cc_final: 0.8759 (tp-100) REVERT: E 489 MET cc_start: 0.7283 (OUTLIER) cc_final: 0.6799 (ptm) REVERT: F 129 ARG cc_start: 0.9175 (ptt-90) cc_final: 0.8849 (ptp90) REVERT: F 155 ASP cc_start: 0.8771 (OUTLIER) cc_final: 0.8352 (t0) REVERT: F 166 GLU cc_start: 0.6699 (tm-30) cc_final: 0.6021 (tm-30) REVERT: F 235 ARG cc_start: 0.8871 (mtp85) cc_final: 0.8593 (mtp85) REVERT: F 251 SER cc_start: 0.8625 (t) cc_final: 0.8370 (p) REVERT: F 257 ILE cc_start: 0.9359 (OUTLIER) cc_final: 0.9150 (tp) REVERT: F 403 ASP cc_start: 0.8884 (t0) cc_final: 0.8507 (t0) REVERT: F 463 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8672 (mp) outliers start: 91 outliers final: 55 residues processed: 273 average time/residue: 0.2204 time to fit residues: 104.9991 Evaluate side-chains 252 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 183 time to evaluate : 1.460 ------------------------------------------------------------------------------- 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 247 THR Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 264 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 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 273 ILE Chi-restraints excluded: chain B residue 284 SER Chi-restraints excluded: chain B residue 458 ILE 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 270 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 203 PHE 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 239 LYS 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 468 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 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 29 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 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 489 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 128 optimal weight: 0.9990 chunk 340 optimal weight: 60.0000 chunk 105 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 227 optimal weight: 8.9990 chunk 343 optimal weight: 50.0000 chunk 77 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 187 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 53 optimal weight: 0.0000 overall best weight: 1.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 5 GLN ** 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 = 0.3651 r_free = 0.3651 target = 0.068746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.049973 restraints weight = 219889.741| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 3.32 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.076 48571 Z= 0.115 Angle : 0.479 12.232 70240 Z= 0.268 Chirality : 0.036 0.368 8517 Planarity : 0.003 0.037 5277 Dihedral : 23.600 178.880 18856 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 3.52 % Allowed : 19.48 % Favored : 77.00 % 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: 2.08 (0.16), residues: 2964 helix: 2.67 (0.13), residues: 1644 sheet: -1.59 (0.29), residues: 252 loop : 0.13 (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 0.022 0.001 PHE B 303 TRP 0.011 0.001 TRP C 250 HIS 0.016 0.001 HIS B 146 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.11 (48571) covalent geometry : angle 0.47882 / 0.27 (70240) hydrogen bonds : bond 0.06487 / 4.18 ( 2142) hydrogen bonds : angle 4.12514 / 2.94 ( 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 293 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 198 time to evaluate : 1.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 164 LEU cc_start: 0.9045 (pt) cc_final: 0.8782 (tp) REVERT: A 196 GLU cc_start: 0.8702 (mt-10) cc_final: 0.8453 (mt-10) REVERT: A 232 ASP cc_start: 0.9115 (t70) cc_final: 0.8795 (t0) REVERT: A 284 SER cc_start: 0.9006 (m) cc_final: 0.8752 (t) REVERT: A 392 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.6936 (ptmt) REVERT: B 155 ASP cc_start: 0.8915 (OUTLIER) cc_final: 0.8711 (t70) REVERT: B 184 GLN cc_start: 0.8476 (mt0) cc_final: 0.8224 (tt0) REVERT: B 187 GLU cc_start: 0.8730 (mm-30) cc_final: 0.8226 (mp0) REVERT: B 228 LYS cc_start: 0.9192 (tppt) cc_final: 0.8816 (tppt) REVERT: B 232 ASP cc_start: 0.8798 (m-30) cc_final: 0.8307 (m-30) REVERT: B 236 GLU cc_start: 0.9115 (tp30) cc_final: 0.8544 (tp30) REVERT: B 267 PHE cc_start: 0.8821 (t80) cc_final: 0.8556 (t80) REVERT: B 364 GLU cc_start: 0.8995 (tp30) cc_final: 0.8790 (tp30) REVERT: B 395 MET cc_start: 0.8973 (tpp) cc_final: 0.8736 (tpp) REVERT: B 458 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8858 (pt) REVERT: C 1 MET cc_start: 0.8087 (tmm) cc_final: 0.7822 (tmm) REVERT: C 12 LEU cc_start: 0.9437 (mt) cc_final: 0.9222 (mt) REVERT: C 187 GLU cc_start: 0.9213 (mm-30) cc_final: 0.8549 (mm-30) REVERT: C 232 ASP cc_start: 0.8885 (m-30) cc_final: 0.8617 (m-30) REVERT: C 440 PHE cc_start: 0.9300 (t80) cc_final: 0.9033 (t80) REVERT: C 482 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8834 (tt0) REVERT: D 8 GLN cc_start: 0.8799 (OUTLIER) cc_final: 0.8501 (mp10) REVERT: D 16 LYS cc_start: 0.9419 (OUTLIER) cc_final: 0.9094 (mtmp) REVERT: D 151 ASP cc_start: 0.9514 (t0) cc_final: 0.8897 (t0) REVERT: D 196 GLU cc_start: 0.8897 (mt-10) cc_final: 0.8390 (mt-10) REVERT: D 205 ARG cc_start: 0.8143 (mtp180) cc_final: 0.7905 (mtp85) REVERT: D 239 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.7714 (tptp) REVERT: E 113 ASP cc_start: 0.9463 (m-30) cc_final: 0.9215 (m-30) REVERT: E 155 ASP cc_start: 0.8807 (OUTLIER) cc_final: 0.8090 (t0) REVERT: E 232 ASP cc_start: 0.8985 (m-30) cc_final: 0.8778 (m-30) REVERT: E 251 SER cc_start: 0.9080 (p) cc_final: 0.8841 (p) REVERT: E 252 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8561 (mm-40) REVERT: E 392 LYS cc_start: 0.7391 (OUTLIER) cc_final: 0.6743 (ptpt) REVERT: E 481 GLN cc_start: 0.9258 (OUTLIER) cc_final: 0.8740 (tp-100) REVERT: E 489 MET cc_start: 0.7271 (OUTLIER) cc_final: 0.6719 (ppp) REVERT: F 129 ARG cc_start: 0.9143 (ptt-90) cc_final: 0.8837 (ptp90) REVERT: F 155 ASP cc_start: 0.8708 (OUTLIER) cc_final: 0.8256 (t0) REVERT: F 235 ARG cc_start: 0.8855 (mtp85) cc_final: 0.8552 (mtp85) REVERT: F 251 SER cc_start: 0.8737 (t) cc_final: 0.8336 (p) REVERT: F 403 ASP cc_start: 0.8858 (t0) cc_final: 0.8487 (t0) REVERT: F 463 LEU cc_start: 0.8931 (OUTLIER) cc_final: 0.8349 (tp) outliers start: 95 outliers final: 57 residues processed: 273 average time/residue: 0.2321 time to fit residues: 111.1347 Evaluate side-chains 256 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 186 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 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 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 392 LYS 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 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 273 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 488 ILE 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 264 ILE 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 98 LYS Chi-restraints excluded: chain D residue 145 VAL Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain D residue 203 PHE 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 239 LYS 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 458 ILE 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 252 GLN 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 84 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 339 optimal weight: 50.0000 chunk 324 optimal weight: 50.0000 chunk 88 optimal weight: 0.9980 chunk 383 optimal weight: 50.0000 chunk 112 optimal weight: 4.9990 chunk 236 optimal weight: 4.9990 chunk 385 optimal weight: 40.0000 chunk 214 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** ** E 159 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.068741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.049412 restraints weight = 225113.621| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 3.35 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 48571 Z= 0.132 Angle : 0.488 12.707 70240 Z= 0.271 Chirality : 0.037 0.364 8517 Planarity : 0.003 0.038 5277 Dihedral : 23.565 179.293 18856 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 3.26 % Allowed : 19.81 % Favored : 76.93 % 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: 2.11 (0.16), residues: 2964 helix: 2.70 (0.13), residues: 1644 sheet: -1.53 (0.29), residues: 252 loop : 0.12 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 235 TYR 0.022 0.001 TYR A 329 PHE 0.011 0.001 PHE B 120 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 0.00268 / 0.13 (48571) covalent geometry : angle 0.48844 / 0.27 (70240) hydrogen bonds : bond 0.06489 / 4.19 ( 2142) hydrogen bonds : angle 4.12710 / 2.94 ( 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 281 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 193 time to evaluate : 1.388 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.9075 (pt) cc_final: 0.8787 (tp) REVERT: A 196 GLU cc_start: 0.8713 (mt-10) cc_final: 0.8468 (mt-10) REVERT: A 230 ASP cc_start: 0.8981 (t0) cc_final: 0.8638 (t0) REVERT: A 232 ASP cc_start: 0.9164 (t70) cc_final: 0.8875 (t0) REVERT: A 284 SER cc_start: 0.8994 (m) cc_final: 0.8733 (t) REVERT: A 392 LYS cc_start: 0.7278 (OUTLIER) cc_final: 0.6782 (ptmt) REVERT: B 161 ARG cc_start: 0.8619 (OUTLIER) cc_final: 0.7484 (mtp180) REVERT: B 184 GLN cc_start: 0.8466 (mt0) cc_final: 0.8254 (tt0) REVERT: B 187 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8220 (mp0) REVERT: B 228 LYS cc_start: 0.9187 (tppt) cc_final: 0.8803 (tppt) REVERT: B 232 ASP cc_start: 0.8820 (m-30) cc_final: 0.8319 (m-30) REVERT: B 236 GLU cc_start: 0.9118 (tp30) cc_final: 0.8546 (tp30) REVERT: B 259 ASN cc_start: 0.8763 (m-40) cc_final: 0.8545 (m-40) REVERT: B 267 PHE cc_start: 0.8808 (t80) cc_final: 0.8607 (t80) REVERT: B 364 GLU cc_start: 0.9061 (tp30) cc_final: 0.8846 (tp30) REVERT: B 395 MET cc_start: 0.8987 (tpp) cc_final: 0.8714 (tpp) REVERT: C 1 MET cc_start: 0.8040 (tmm) cc_final: 0.7753 (tmm) REVERT: C 155 ASP cc_start: 0.9067 (OUTLIER) cc_final: 0.8604 (t0) REVERT: C 187 GLU cc_start: 0.9237 (mm-30) cc_final: 0.8560 (mm-30) REVERT: C 232 ASP cc_start: 0.8895 (m-30) cc_final: 0.8596 (m-30) REVERT: C 448 ASP cc_start: 0.9599 (OUTLIER) cc_final: 0.9365 (p0) REVERT: C 482 GLU cc_start: 0.9075 (mt-10) cc_final: 0.8848 (tt0) REVERT: D 8 GLN cc_start: 0.8828 (OUTLIER) cc_final: 0.8536 (mp10) REVERT: D 16 LYS cc_start: 0.9426 (OUTLIER) cc_final: 0.9099 (mtmp) REVERT: D 151 ASP cc_start: 0.9540 (t0) cc_final: 0.8973 (t0) REVERT: D 196 GLU cc_start: 0.8924 (mt-10) cc_final: 0.8424 (mt-10) REVERT: D 205 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7952 (mtp85) REVERT: D 239 LYS cc_start: 0.8749 (OUTLIER) cc_final: 0.7849 (tptp) REVERT: D 448 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8481 (p0) REVERT: E 113 ASP cc_start: 0.9472 (m-30) cc_final: 0.9221 (m-30) REVERT: E 155 ASP cc_start: 0.8822 (OUTLIER) cc_final: 0.8095 (t0) REVERT: E 232 ASP cc_start: 0.9033 (m-30) cc_final: 0.8817 (m-30) REVERT: E 253 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8628 (mt-10) REVERT: E 392 LYS cc_start: 0.7337 (OUTLIER) cc_final: 0.6726 (ptpt) REVERT: E 481 GLN cc_start: 0.9274 (OUTLIER) cc_final: 0.8707 (tp-100) REVERT: E 489 MET cc_start: 0.7426 (ptm) cc_final: 0.6882 (ppp) REVERT: F 129 ARG cc_start: 0.9159 (ptt-90) cc_final: 0.8866 (ptp90) REVERT: F 155 ASP cc_start: 0.8754 (OUTLIER) cc_final: 0.8306 (t0) REVERT: F 166 GLU cc_start: 0.6702 (tm-30) cc_final: 0.6002 (tm-30) REVERT: F 235 ARG cc_start: 0.8873 (mtp85) cc_final: 0.8582 (mtp85) REVERT: F 251 SER cc_start: 0.8569 (t) cc_final: 0.8260 (p) REVERT: F 403 ASP cc_start: 0.8911 (t0) cc_final: 0.8533 (t0) REVERT: F 448 ASP cc_start: 0.9271 (OUTLIER) cc_final: 0.8579 (p0) REVERT: F 463 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8367 (tp) outliers start: 88 outliers final: 59 residues processed: 262 average time/residue: 0.2376 time to fit residues: 108.7166 Evaluate side-chains 256 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 183 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 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 251 SER 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 392 LYS 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 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 273 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain C residue 116 ILE Chi-restraints excluded: chain C residue 152 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 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 16 LYS 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 203 PHE 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 239 LYS 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 458 ILE 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 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 29 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 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 463 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 489 MET 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: 50.0000 chunk 0 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 226 optimal weight: 0.1980 chunk 170 optimal weight: 10.0000 chunk 261 optimal weight: 3.9990 chunk 214 optimal weight: 1.9990 chunk 366 optimal weight: 50.0000 chunk 342 optimal weight: 50.0000 overall best weight: 2.4388 ------------------------------------------------------------------------------- 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** ** E 159 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.068897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.049588 restraints weight = 223277.107| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 3.34 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 48571 Z= 0.118 Angle : 0.482 12.569 70240 Z= 0.268 Chirality : 0.036 0.366 8517 Planarity : 0.003 0.039 5277 Dihedral : 23.528 179.372 18853 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 2.81 % Allowed : 20.52 % Favored : 76.67 % 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: 2.11 (0.16), residues: 2964 helix: 2.70 (0.13), residues: 1644 sheet: -1.49 (0.29), residues: 252 loop : 0.12 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 39 TYR 0.026 0.001 TYR E 381 PHE 0.017 0.001 PHE D 240 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 0.00236 / 0.12 (48571) covalent geometry : angle 0.48202 / 0.27 (70240) hydrogen bonds : bond 0.06405 / 4.12 ( 2142) hydrogen bonds : angle 4.10073 / 2.92 ( 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: 76 poor density : 199 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 164 LEU cc_start: 0.9064 (pt) cc_final: 0.8798 (tp) REVERT: A 196 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8454 (mt-10) REVERT: A 230 ASP cc_start: 0.8971 (t0) cc_final: 0.8605 (t0) REVERT: A 232 ASP cc_start: 0.9171 (t70) cc_final: 0.8869 (t0) REVERT: A 284 SER cc_start: 0.8990 (m) cc_final: 0.8729 (t) REVERT: A 392 LYS cc_start: 0.7181 (OUTLIER) cc_final: 0.6715 (ptmt) REVERT: B 161 ARG cc_start: 0.8622 (OUTLIER) cc_final: 0.7451 (mtp180) REVERT: B 184 GLN cc_start: 0.8534 (mt0) cc_final: 0.8280 (tt0) REVERT: B 187 GLU cc_start: 0.8727 (mm-30) cc_final: 0.8227 (mp0) REVERT: B 228 LYS cc_start: 0.9185 (tppt) cc_final: 0.8827 (tppt) REVERT: B 232 ASP cc_start: 0.8836 (m-30) cc_final: 0.8337 (m-30) REVERT: B 236 GLU cc_start: 0.9116 (tp30) cc_final: 0.8536 (tp30) REVERT: B 259 ASN cc_start: 0.8754 (m-40) cc_final: 0.8538 (m-40) REVERT: B 267 PHE cc_start: 0.8820 (t80) cc_final: 0.8618 (t80) REVERT: B 364 GLU cc_start: 0.9074 (tp30) cc_final: 0.8850 (tp30) REVERT: B 413 TRP cc_start: 0.9205 (t60) cc_final: 0.8976 (t60) REVERT: B 458 ILE cc_start: 0.9111 (OUTLIER) cc_final: 0.8864 (pt) REVERT: C 1 MET cc_start: 0.8004 (tmm) cc_final: 0.7697 (tmm) REVERT: C 155 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8631 (t0) REVERT: C 187 GLU cc_start: 0.9242 (mm-30) cc_final: 0.8563 (mm-30) REVERT: C 232 ASP cc_start: 0.8903 (m-30) cc_final: 0.8621 (m-30) REVERT: C 448 ASP cc_start: 0.9620 (OUTLIER) cc_final: 0.9331 (p0) REVERT: C 482 GLU cc_start: 0.9070 (mt-10) cc_final: 0.8837 (tt0) REVERT: D 8 GLN cc_start: 0.8846 (OUTLIER) cc_final: 0.8542 (mp10) REVERT: D 16 LYS cc_start: 0.9416 (OUTLIER) cc_final: 0.9094 (mtmp) REVERT: D 151 ASP cc_start: 0.9518 (t0) cc_final: 0.9049 (t0) REVERT: D 196 GLU cc_start: 0.8917 (mt-10) cc_final: 0.8407 (mt-10) REVERT: D 205 ARG cc_start: 0.8261 (mtp180) cc_final: 0.8027 (mtp85) REVERT: D 239 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.7925 (tptp) REVERT: D 253 GLU cc_start: 0.8952 (mt-10) cc_final: 0.8578 (pm20) REVERT: D 448 ASP cc_start: 0.9073 (OUTLIER) cc_final: 0.8455 (p0) REVERT: E 113 ASP cc_start: 0.9479 (m-30) cc_final: 0.9222 (m-30) REVERT: E 155 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8104 (t0) REVERT: E 232 ASP cc_start: 0.9004 (m-30) cc_final: 0.8795 (m-30) REVERT: E 253 GLU cc_start: 0.8794 (mt-10) cc_final: 0.8391 (mt-10) REVERT: E 392 LYS cc_start: 0.7304 (OUTLIER) cc_final: 0.6323 (ttpt) REVERT: F 129 ARG cc_start: 0.9146 (ptt-90) cc_final: 0.8868 (ptp90) REVERT: F 155 ASP cc_start: 0.8727 (OUTLIER) cc_final: 0.8276 (t0) REVERT: F 166 GLU cc_start: 0.6728 (tm-30) cc_final: 0.6045 (tm-30) REVERT: F 235 ARG cc_start: 0.8910 (mtp85) cc_final: 0.8620 (mtp85) REVERT: F 251 SER cc_start: 0.8691 (t) cc_final: 0.8285 (p) REVERT: F 403 ASP cc_start: 0.8897 (t0) cc_final: 0.8524 (t0) REVERT: F 463 LEU cc_start: 0.8929 (OUTLIER) cc_final: 0.8364 (tp) outliers start: 76 outliers final: 54 residues processed: 257 average time/residue: 0.1865 time to fit residues: 83.1932 Evaluate side-chains 256 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 189 time to evaluate : 0.741 ------------------------------------------------------------------------------- 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 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 229 LEU Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 SER 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 392 LYS 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 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 273 ILE Chi-restraints excluded: chain B residue 458 ILE Chi-restraints excluded: chain B residue 488 ILE Chi-restraints excluded: chain C residue 152 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 284 SER Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain D residue 8 GLN Chi-restraints excluded: chain D residue 16 LYS 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 203 PHE Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 239 LYS 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 458 ILE 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 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 29 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 390 random chunks: chunk 84 optimal weight: 9.9990 chunk 257 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 146 optimal weight: 10.0000 chunk 246 optimal weight: 1.9990 chunk 327 optimal weight: 50.0000 chunk 88 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 chunk 351 optimal weight: 50.0000 chunk 263 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** E 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN ** 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 = 0.3639 r_free = 0.3639 target = 0.068019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.049378 restraints weight = 222197.700| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.33 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.3408 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= 0.152 Angle : 0.497 12.850 70240 Z= 0.275 Chirality : 0.037 0.362 8517 Planarity : 0.004 0.039 5277 Dihedral : 23.527 179.814 18853 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.85 % Allowed : 20.67 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.13 (0.16), residues: 2964 helix: 2.68 (0.13), residues: 1638 sheet: -1.41 (0.30), residues: 252 loop : 0.18 (0.21), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 39 TYR 0.025 0.001 TYR C 370 PHE 0.012 0.001 PHE B 120 TRP 0.016 0.001 TRP C 250 HIS 0.008 0.001 HIS B 26 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (48571) covalent geometry : angle 0.49672 / 0.27 (70240) hydrogen bonds : bond 0.06603 / 4.25 ( 2142) hydrogen bonds : angle 4.13956 / 2.95 ( 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 264 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 187 time to evaluate : 0.772 Fit side-chains revert: symmetry clash REVERT: A 196 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8429 (mt-10) REVERT: A 230 ASP cc_start: 0.8882 (OUTLIER) cc_final: 0.8580 (t0) REVERT: A 232 ASP cc_start: 0.9166 (t70) cc_final: 0.8851 (t0) REVERT: A 235 ARG cc_start: 0.8082 (mtt180) cc_final: 0.7726 (mtt90) REVERT: A 392 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6725 (ptmt) REVERT: B 161 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7535 (mtp180) REVERT: B 187 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8318 (mp0) REVERT: B 228 LYS cc_start: 0.9188 (tppt) cc_final: 0.8822 (tppt) REVERT: B 232 ASP cc_start: 0.8819 (m-30) cc_final: 0.8354 (m-30) REVERT: B 236 GLU cc_start: 0.9114 (tp30) cc_final: 0.8535 (tp30) REVERT: B 259 ASN cc_start: 0.8779 (m-40) cc_final: 0.8571 (m-40) REVERT: B 267 PHE cc_start: 0.8861 (t80) cc_final: 0.8601 (t80) REVERT: B 364 GLU cc_start: 0.9071 (tp30) cc_final: 0.8862 (tp30) REVERT: C 1 MET cc_start: 0.8081 (tmm) cc_final: 0.7765 (tmm) REVERT: C 155 ASP cc_start: 0.8922 (OUTLIER) cc_final: 0.8611 (t0) REVERT: C 232 ASP cc_start: 0.8897 (m-30) cc_final: 0.8594 (m-30) REVERT: C 448 ASP cc_start: 0.9631 (OUTLIER) cc_final: 0.9345 (p0) REVERT: C 482 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8828 (tt0) REVERT: D 8 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8575 (mp10) REVERT: D 151 ASP cc_start: 0.9511 (t0) cc_final: 0.9020 (t0) REVERT: D 196 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8457 (mt-10) REVERT: D 205 ARG cc_start: 0.8248 (mtp180) cc_final: 0.8017 (mtp85) REVERT: D 239 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8002 (tptp) REVERT: D 448 ASP cc_start: 0.9087 (OUTLIER) cc_final: 0.8483 (p0) REVERT: E 113 ASP cc_start: 0.9482 (m-30) cc_final: 0.9189 (m-30) REVERT: E 155 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8005 (t0) REVERT: E 253 GLU cc_start: 0.8772 (mt-10) cc_final: 0.8390 (mt-10) REVERT: E 392 LYS cc_start: 0.7377 (OUTLIER) cc_final: 0.6387 (ttpt) REVERT: F 129 ARG cc_start: 0.9128 (ptt-90) cc_final: 0.8847 (ptp90) REVERT: F 155 ASP cc_start: 0.8746 (OUTLIER) cc_final: 0.8344 (t0) REVERT: F 166 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6160 (tm-30) REVERT: F 235 ARG cc_start: 0.8856 (mtp85) cc_final: 0.8571 (mtp85) REVERT: F 251 SER cc_start: 0.8783 (t) cc_final: 0.8343 (p) REVERT: F 403 ASP cc_start: 0.8897 (t0) cc_final: 0.8567 (t0) REVERT: F 448 ASP cc_start: 0.9261 (OUTLIER) cc_final: 0.8611 (p0) REVERT: F 463 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8412 (tp) outliers start: 77 outliers final: 58 residues processed: 247 average time/residue: 0.1598 time to fit residues: 68.8575 Evaluate side-chains 253 residues out of total 2718 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 182 time to evaluate : 0.739 ------------------------------------------------------------------------------- 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 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 229 LEU Chi-restraints excluded: chain A residue 230 ASP Chi-restraints excluded: chain A residue 247 THR Chi-restraints excluded: chain A residue 251 SER 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 392 LYS 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 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 488 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 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 155 ASP Chi-restraints excluded: chain D residue 181 LEU Chi-restraints excluded: chain D residue 226 CYS Chi-restraints excluded: chain D residue 233 LEU Chi-restraints excluded: chain D residue 239 LYS 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 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 116 ILE 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 263 ILE Chi-restraints excluded: chain F residue 289 LYS Chi-restraints excluded: chain F residue 360 ILE Chi-restraints excluded: chain F residue 428 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 463 LEU Chi-restraints excluded: chain F residue 468 SER Chi-restraints excluded: chain F residue 489 MET 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: 0.8980 chunk 283 optimal weight: 8.9990 chunk 155 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 308 optimal weight: 50.0000 chunk 263 optimal weight: 0.9990 chunk 180 optimal weight: 5.9990 chunk 329 optimal weight: 50.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 146 HIS ** 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 178 HIS ** 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 = 0.3636 r_free = 0.3636 target = 0.067807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.049256 restraints weight = 222609.358| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 3.33 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.3574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 48571 Z= 0.147 Angle : 0.496 12.628 70240 Z= 0.275 Chirality : 0.037 0.361 8517 Planarity : 0.004 0.040 5277 Dihedral : 23.555 179.595 18853 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.96 % Allowed : 20.81 % 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: 2.08 (0.16), residues: 2964 helix: 2.64 (0.13), residues: 1644 sheet: -1.38 (0.30), residues: 252 loop : 0.12 (0.21), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 39 TYR 0.027 0.001 TYR A 254 PHE 0.016 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 0.00299 / 0.15 (48571) covalent geometry : angle 0.49564 / 0.28 (70240) hydrogen bonds : bond 0.06658 / 4.27 ( 2142) hydrogen bonds : angle 4.14689 / 2.95 ( 4948) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6043.06 seconds wall clock time: 106 minutes 11.80 seconds (6371.80 seconds total)