Starting phenix.real_space_refine (version: dev) on Wed Dec 21 14:38:58 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/12_2022/7tf6_25863.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/12_2022/7tf6_25863.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/12_2022/7tf6_25863.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/12_2022/7tf6_25863.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/12_2022/7tf6_25863.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7tf6_25863/12_2022/7tf6_25863.pdb" } resolution = 2.15 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.112 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "L GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 43272 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "B" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "D" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "E" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "F" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "G" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "H" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "J" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "K" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "L" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "M" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "N" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "O" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "P" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "Q" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "R" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "S" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "T" Number of atoms: 3494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3494 Classifications: {'peptide': 438} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 23, 'TRANS': 414} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 5} Unresolved non-hydrogen planarities: 20 Chain: "U" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "V" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "W" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "X" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 90 Classifications: {'peptide': 11} Link IDs: {'TRANS': 10} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "G" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "H" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "L" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "N" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "O" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "S" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Chain: "T" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 22 Unusual residues: {' MG': 2} Classifications: {'peptide': 1, 'undetermined': 2} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N LEU A 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU A 252 " occ=0.97 residue: pdb=" N LEU B 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU B 252 " occ=0.97 residue: pdb=" N LEU C 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU C 252 " occ=0.97 residue: pdb=" N LEU F 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU F 252 " occ=0.97 residue: pdb=" N LEU G 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU G 252 " occ=0.97 residue: pdb=" N LEU H 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU H 252 " occ=0.97 residue: pdb=" N LEU L 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU L 252 " occ=0.97 residue: pdb=" N LEU N 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU N 252 " occ=0.97 residue: pdb=" N LEU O 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU O 252 " occ=0.97 residue: pdb=" N LEU R 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU R 252 " occ=0.97 residue: pdb=" N LEU S 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU S 252 " occ=0.97 residue: pdb=" N LEU T 252 " occ=0.97 ... (6 atoms not shown) pdb=" CD2 LEU T 252 " occ=0.97 Time building chain proxies: 22.80, per 1000 atoms: 0.53 Number of scatterers: 43272 At special positions: 0 Unit cell: (150.48, 159.28, 124.08, 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 204 16.00 Mg 24 11.99 O 8160 8.00 N 7296 7.00 C 27468 6.00 H 120 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.86 Conformation dependent library (CDL) restraints added in 7.8 seconds 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10104 Finding SS restraints... Secondary structure from input PDB file: 226 helices and 24 sheets defined 44.1% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'A' and resid 7 through 19 Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 56 through 64 removed outlier: 6.495A pdb=" N PHE A 62 " --> pdb=" O ILE A 59 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N VAL A 63 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ARG A 64 " --> pdb=" O GLY A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 79 Processing helix chain 'A' and resid 109 through 123 removed outlier: 3.692A pdb=" N ASP A 123 " --> pdb=" O LYS A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 182 Processing helix chain 'A' and resid 206 through 227 Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 287 through 292 Processing helix chain 'A' and resid 296 through 301 removed outlier: 3.610A pdb=" N ARG A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 332 removed outlier: 3.826A pdb=" N THR A 332 " --> pdb=" O GLY A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 363 Processing helix chain 'A' and resid 378 through 386 Processing helix chain 'A' and resid 393 through 402 Processing helix chain 'A' and resid 404 through 412 removed outlier: 3.969A pdb=" N LYS A 408 " --> pdb=" O ASN A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 432 removed outlier: 3.786A pdb=" N THR A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 442 Processing helix chain 'B' and resid 7 through 19 Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 56 through 64 removed outlier: 6.501A pdb=" N PHE B 62 " --> pdb=" O ILE B 59 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 63 " --> pdb=" O GLU B 60 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ARG B 64 " --> pdb=" O GLY B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 79 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 123 through 125 No H-bonds generated for 'chain 'B' and resid 123 through 125' Processing helix chain 'B' and resid 169 through 182 Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'B' and resid 270 through 283 Processing helix chain 'B' and resid 287 through 292 Processing helix chain 'B' and resid 296 through 301 removed outlier: 3.554A pdb=" N ARG B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 332 removed outlier: 3.878A pdb=" N THR B 332 " --> pdb=" O GLY B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 344 through 363 Processing helix chain 'B' and resid 378 through 386 Processing helix chain 'B' and resid 393 through 402 Processing helix chain 'B' and resid 404 through 412 removed outlier: 3.977A pdb=" N LYS B 408 " --> pdb=" O ASN B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 432 removed outlier: 3.790A pdb=" N THR B 432 " --> pdb=" O ASP B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 442 Processing helix chain 'C' and resid 7 through 19 Processing helix chain 'C' and resid 43 through 49 Processing helix chain 'C' and resid 56 through 64 removed outlier: 6.516A pdb=" N PHE C 62 " --> pdb=" O ILE C 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL C 63 " --> pdb=" O GLU C 60 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG C 64 " --> pdb=" O GLY C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 79 Processing helix chain 'C' and resid 109 through 122 Processing helix chain 'C' and resid 123 through 125 No H-bonds generated for 'chain 'C' and resid 123 through 125' Processing helix chain 'C' and resid 169 through 181 Processing helix chain 'C' and resid 206 through 227 Processing helix chain 'C' and resid 270 through 283 Processing helix chain 'C' and resid 287 through 292 Processing helix chain 'C' and resid 296 through 301 removed outlier: 3.581A pdb=" N ARG C 300 " --> pdb=" O ASN C 296 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 332 removed outlier: 3.900A pdb=" N THR C 332 " --> pdb=" O GLY C 329 " (cutoff:3.500A) Processing helix chain 'C' and resid 344 through 363 Processing helix chain 'C' and resid 378 through 386 Processing helix chain 'C' and resid 393 through 402 Processing helix chain 'C' and resid 404 through 412 removed outlier: 3.997A pdb=" N LYS C 408 " --> pdb=" O ASN C 404 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 432 removed outlier: 3.784A pdb=" N THR C 432 " --> pdb=" O ASP C 428 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 442 Processing helix chain 'D' and resid 4 through 8 removed outlier: 3.661A pdb=" N SER D 8 " --> pdb=" O GLY D 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 3.716A pdb=" N SER E 8 " --> pdb=" O GLY E 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 7 through 19 Processing helix chain 'F' and resid 43 through 49 Processing helix chain 'F' and resid 56 through 64 removed outlier: 6.499A pdb=" N PHE F 62 " --> pdb=" O ILE F 59 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL F 63 " --> pdb=" O GLU F 60 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ARG F 64 " --> pdb=" O GLY F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 79 Processing helix chain 'F' and resid 109 through 123 removed outlier: 3.691A pdb=" N ASP F 123 " --> pdb=" O LYS F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 169 through 182 Processing helix chain 'F' and resid 206 through 227 Processing helix chain 'F' and resid 270 through 283 Processing helix chain 'F' and resid 287 through 292 Processing helix chain 'F' and resid 296 through 301 removed outlier: 3.602A pdb=" N ARG F 300 " --> pdb=" O ASN F 296 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 332 removed outlier: 3.850A pdb=" N THR F 332 " --> pdb=" O GLY F 329 " (cutoff:3.500A) Processing helix chain 'F' and resid 344 through 363 Processing helix chain 'F' and resid 378 through 386 Processing helix chain 'F' and resid 393 through 402 Processing helix chain 'F' and resid 404 through 412 removed outlier: 3.965A pdb=" N LYS F 408 " --> pdb=" O ASN F 404 " (cutoff:3.500A) Processing helix chain 'F' and resid 412 through 432 removed outlier: 3.782A pdb=" N THR F 432 " --> pdb=" O ASP F 428 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 442 Processing helix chain 'G' and resid 7 through 19 Processing helix chain 'G' and resid 43 through 49 Processing helix chain 'G' and resid 56 through 64 removed outlier: 6.503A pdb=" N PHE G 62 " --> pdb=" O ILE G 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 63 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG G 64 " --> pdb=" O GLY G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 79 Processing helix chain 'G' and resid 109 through 122 Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 169 through 182 Processing helix chain 'G' and resid 206 through 227 Processing helix chain 'G' and resid 270 through 283 Processing helix chain 'G' and resid 287 through 292 Processing helix chain 'G' and resid 296 through 301 removed outlier: 3.552A pdb=" N ARG G 300 " --> pdb=" O ASN G 296 " (cutoff:3.500A) Processing helix chain 'G' and resid 328 through 332 removed outlier: 3.877A pdb=" N THR G 332 " --> pdb=" O GLY G 329 " (cutoff:3.500A) Processing helix chain 'G' and resid 344 through 363 Processing helix chain 'G' and resid 378 through 386 Processing helix chain 'G' and resid 393 through 402 Processing helix chain 'G' and resid 404 through 412 removed outlier: 3.976A pdb=" N LYS G 408 " --> pdb=" O ASN G 404 " (cutoff:3.500A) Processing helix chain 'G' and resid 412 through 432 removed outlier: 3.808A pdb=" N THR G 432 " --> pdb=" O ASP G 428 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 442 Processing helix chain 'H' and resid 7 through 19 Processing helix chain 'H' and resid 43 through 49 Processing helix chain 'H' and resid 56 through 64 removed outlier: 6.511A pdb=" N PHE H 62 " --> pdb=" O ILE H 59 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N VAL H 63 " --> pdb=" O GLU H 60 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG H 64 " --> pdb=" O GLY H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 79 Processing helix chain 'H' and resid 109 through 122 Processing helix chain 'H' and resid 123 through 125 No H-bonds generated for 'chain 'H' and resid 123 through 125' Processing helix chain 'H' and resid 169 through 181 Processing helix chain 'H' and resid 206 through 227 Processing helix chain 'H' and resid 270 through 283 Processing helix chain 'H' and resid 287 through 292 Processing helix chain 'H' and resid 296 through 301 removed outlier: 3.581A pdb=" N ARG H 300 " --> pdb=" O ASN H 296 " (cutoff:3.500A) Processing helix chain 'H' and resid 328 through 332 removed outlier: 3.851A pdb=" N THR H 332 " --> pdb=" O GLY H 329 " (cutoff:3.500A) Processing helix chain 'H' and resid 344 through 363 Processing helix chain 'H' and resid 378 through 386 Processing helix chain 'H' and resid 393 through 402 Processing helix chain 'H' and resid 404 through 412 removed outlier: 3.988A pdb=" N LYS H 408 " --> pdb=" O ASN H 404 " (cutoff:3.500A) Processing helix chain 'H' and resid 412 through 432 removed outlier: 3.782A pdb=" N THR H 432 " --> pdb=" O ASP H 428 " (cutoff:3.500A) Processing helix chain 'H' and resid 435 through 442 Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.719A pdb=" N SER I 8 " --> pdb=" O GLY I 5 " (cutoff:3.500A) Processing helix chain 'J' and resid 4 through 8 removed outlier: 3.675A pdb=" N SER J 8 " --> pdb=" O GLY J 5 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 8 removed outlier: 3.660A pdb=" N SER K 8 " --> pdb=" O GLY K 5 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 19 Processing helix chain 'L' and resid 43 through 49 Processing helix chain 'L' and resid 56 through 64 removed outlier: 6.507A pdb=" N PHE L 62 " --> pdb=" O ILE L 59 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL L 63 " --> pdb=" O GLU L 60 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG L 64 " --> pdb=" O GLY L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 79 Processing helix chain 'L' and resid 109 through 122 Processing helix chain 'L' and resid 123 through 125 No H-bonds generated for 'chain 'L' and resid 123 through 125' Processing helix chain 'L' and resid 169 through 181 Processing helix chain 'L' and resid 206 through 227 Processing helix chain 'L' and resid 270 through 283 Processing helix chain 'L' and resid 287 through 292 Processing helix chain 'L' and resid 296 through 301 removed outlier: 3.602A pdb=" N ARG L 300 " --> pdb=" O ASN L 296 " (cutoff:3.500A) Processing helix chain 'L' and resid 328 through 332 removed outlier: 3.853A pdb=" N THR L 332 " --> pdb=" O GLY L 329 " (cutoff:3.500A) Processing helix chain 'L' and resid 344 through 363 Processing helix chain 'L' and resid 378 through 386 Processing helix chain 'L' and resid 393 through 402 Processing helix chain 'L' and resid 404 through 412 removed outlier: 3.969A pdb=" N LYS L 408 " --> pdb=" O ASN L 404 " (cutoff:3.500A) Processing helix chain 'L' and resid 412 through 432 removed outlier: 3.791A pdb=" N THR L 432 " --> pdb=" O ASP L 428 " (cutoff:3.500A) Processing helix chain 'L' and resid 435 through 442 Processing helix chain 'M' and resid 4 through 8 removed outlier: 3.697A pdb=" N SER M 8 " --> pdb=" O GLY M 5 " (cutoff:3.500A) Processing helix chain 'N' and resid 7 through 19 Processing helix chain 'N' and resid 43 through 49 Processing helix chain 'N' and resid 56 through 64 removed outlier: 6.492A pdb=" N PHE N 62 " --> pdb=" O ILE N 59 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL N 63 " --> pdb=" O GLU N 60 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG N 64 " --> pdb=" O GLY N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 76 through 79 Processing helix chain 'N' and resid 109 through 122 Processing helix chain 'N' and resid 123 through 125 No H-bonds generated for 'chain 'N' and resid 123 through 125' Processing helix chain 'N' and resid 169 through 182 Processing helix chain 'N' and resid 206 through 227 Processing helix chain 'N' and resid 270 through 283 Processing helix chain 'N' and resid 287 through 292 Processing helix chain 'N' and resid 296 through 301 removed outlier: 3.554A pdb=" N ARG N 300 " --> pdb=" O ASN N 296 " (cutoff:3.500A) Processing helix chain 'N' and resid 328 through 332 removed outlier: 3.876A pdb=" N THR N 332 " --> pdb=" O GLY N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 344 through 363 Processing helix chain 'N' and resid 378 through 386 Processing helix chain 'N' and resid 393 through 402 Processing helix chain 'N' and resid 404 through 412 removed outlier: 3.977A pdb=" N LYS N 408 " --> pdb=" O ASN N 404 " (cutoff:3.500A) Processing helix chain 'N' and resid 412 through 432 removed outlier: 3.807A pdb=" N THR N 432 " --> pdb=" O ASP N 428 " (cutoff:3.500A) Processing helix chain 'N' and resid 435 through 442 Processing helix chain 'O' and resid 7 through 19 Processing helix chain 'O' and resid 43 through 49 Processing helix chain 'O' and resid 56 through 64 removed outlier: 6.515A pdb=" N PHE O 62 " --> pdb=" O ILE O 59 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL O 63 " --> pdb=" O GLU O 60 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ARG O 64 " --> pdb=" O GLY O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 79 Processing helix chain 'O' and resid 109 through 122 Processing helix chain 'O' and resid 123 through 125 No H-bonds generated for 'chain 'O' and resid 123 through 125' Processing helix chain 'O' and resid 169 through 181 Processing helix chain 'O' and resid 206 through 227 Processing helix chain 'O' and resid 270 through 283 Processing helix chain 'O' and resid 287 through 292 Processing helix chain 'O' and resid 296 through 301 removed outlier: 3.581A pdb=" N ARG O 300 " --> pdb=" O ASN O 296 " (cutoff:3.500A) Processing helix chain 'O' and resid 328 through 332 removed outlier: 3.853A pdb=" N THR O 332 " --> pdb=" O GLY O 329 " (cutoff:3.500A) Processing helix chain 'O' and resid 344 through 363 Processing helix chain 'O' and resid 378 through 386 Processing helix chain 'O' and resid 393 through 402 Processing helix chain 'O' and resid 404 through 412 removed outlier: 3.986A pdb=" N LYS O 408 " --> pdb=" O ASN O 404 " (cutoff:3.500A) Processing helix chain 'O' and resid 412 through 432 removed outlier: 3.791A pdb=" N THR O 432 " --> pdb=" O ASP O 428 " (cutoff:3.500A) Processing helix chain 'O' and resid 435 through 442 Processing helix chain 'P' and resid 4 through 8 removed outlier: 3.694A pdb=" N SER P 8 " --> pdb=" O GLY P 5 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 8 removed outlier: 3.714A pdb=" N SER Q 8 " --> pdb=" O GLY Q 5 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 19 Processing helix chain 'R' and resid 43 through 49 Processing helix chain 'R' and resid 56 through 64 removed outlier: 6.520A pdb=" N PHE R 62 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL R 63 " --> pdb=" O GLU R 60 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG R 64 " --> pdb=" O GLY R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 76 through 79 Processing helix chain 'R' and resid 109 through 122 Processing helix chain 'R' and resid 123 through 125 No H-bonds generated for 'chain 'R' and resid 123 through 125' Processing helix chain 'R' and resid 169 through 182 Processing helix chain 'R' and resid 206 through 227 Processing helix chain 'R' and resid 270 through 283 Processing helix chain 'R' and resid 287 through 292 Processing helix chain 'R' and resid 296 through 301 removed outlier: 3.600A pdb=" N ARG R 300 " --> pdb=" O ASN R 296 " (cutoff:3.500A) Processing helix chain 'R' and resid 328 through 332 removed outlier: 3.850A pdb=" N THR R 332 " --> pdb=" O GLY R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 363 Processing helix chain 'R' and resid 371 through 375 removed outlier: 3.505A pdb=" N TYR R 375 " --> pdb=" O GLN R 372 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 386 Processing helix chain 'R' and resid 393 through 402 Processing helix chain 'R' and resid 404 through 412 removed outlier: 3.970A pdb=" N LYS R 408 " --> pdb=" O ASN R 404 " (cutoff:3.500A) Processing helix chain 'R' and resid 412 through 432 removed outlier: 3.801A pdb=" N THR R 432 " --> pdb=" O ASP R 428 " (cutoff:3.500A) Processing helix chain 'R' and resid 435 through 442 Processing helix chain 'S' and resid 7 through 19 Processing helix chain 'S' and resid 43 through 49 Processing helix chain 'S' and resid 56 through 64 removed outlier: 6.505A pdb=" N PHE S 62 " --> pdb=" O ILE S 59 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL S 63 " --> pdb=" O GLU S 60 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG S 64 " --> pdb=" O GLY S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 76 through 79 Processing helix chain 'S' and resid 109 through 123 removed outlier: 3.685A pdb=" N ASP S 123 " --> pdb=" O LYS S 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 169 through 182 Processing helix chain 'S' and resid 206 through 227 Processing helix chain 'S' and resid 270 through 283 Processing helix chain 'S' and resid 287 through 292 Processing helix chain 'S' and resid 296 through 301 removed outlier: 3.560A pdb=" N ARG S 300 " --> pdb=" O ASN S 296 " (cutoff:3.500A) Processing helix chain 'S' and resid 328 through 332 removed outlier: 3.851A pdb=" N THR S 332 " --> pdb=" O GLY S 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 344 through 363 Processing helix chain 'S' and resid 378 through 386 Processing helix chain 'S' and resid 393 through 402 Processing helix chain 'S' and resid 404 through 412 removed outlier: 3.970A pdb=" N LYS S 408 " --> pdb=" O ASN S 404 " (cutoff:3.500A) Processing helix chain 'S' and resid 412 through 432 removed outlier: 3.812A pdb=" N THR S 432 " --> pdb=" O ASP S 428 " (cutoff:3.500A) Processing helix chain 'S' and resid 435 through 442 Processing helix chain 'T' and resid 7 through 19 Processing helix chain 'T' and resid 43 through 49 Processing helix chain 'T' and resid 56 through 64 removed outlier: 6.515A pdb=" N PHE T 62 " --> pdb=" O ILE T 59 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N VAL T 63 " --> pdb=" O GLU T 60 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG T 64 " --> pdb=" O GLY T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 76 through 79 Processing helix chain 'T' and resid 109 through 122 Processing helix chain 'T' and resid 123 through 125 No H-bonds generated for 'chain 'T' and resid 123 through 125' Processing helix chain 'T' and resid 169 through 181 Processing helix chain 'T' and resid 206 through 227 Processing helix chain 'T' and resid 270 through 283 Processing helix chain 'T' and resid 287 through 292 Processing helix chain 'T' and resid 296 through 301 removed outlier: 3.577A pdb=" N ARG T 300 " --> pdb=" O ASN T 296 " (cutoff:3.500A) Processing helix chain 'T' and resid 328 through 332 removed outlier: 3.852A pdb=" N THR T 332 " --> pdb=" O GLY T 329 " (cutoff:3.500A) Processing helix chain 'T' and resid 344 through 363 Processing helix chain 'T' and resid 378 through 386 Processing helix chain 'T' and resid 393 through 402 Processing helix chain 'T' and resid 404 through 412 removed outlier: 3.994A pdb=" N LYS T 408 " --> pdb=" O ASN T 404 " (cutoff:3.500A) Processing helix chain 'T' and resid 412 through 432 removed outlier: 3.790A pdb=" N THR T 432 " --> pdb=" O ASP T 428 " (cutoff:3.500A) Processing helix chain 'T' and resid 435 through 442 Processing helix chain 'U' and resid 4 through 8 removed outlier: 3.712A pdb=" N SER U 8 " --> pdb=" O GLY U 5 " (cutoff:3.500A) Processing helix chain 'V' and resid 4 through 8 removed outlier: 3.687A pdb=" N SER V 8 " --> pdb=" O GLY V 5 " (cutoff:3.500A) Processing helix chain 'W' and resid 4 through 8 removed outlier: 3.728A pdb=" N SER W 8 " --> pdb=" O GLY W 5 " (cutoff:3.500A) Processing helix chain 'X' and resid 4 through 8 removed outlier: 3.724A pdb=" N SER X 8 " --> pdb=" O GLY X 5 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 34 through 40 current: chain 'A' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 70 through 74 current: chain 'A' and resid 90 through 99 Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 142 removed outlier: 5.268A pdb=" N GLU A 151 " --> pdb=" O LYS A 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 148 through 152 current: chain 'A' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 196 through 201 current: chain 'A' and resid 322 through 323 Processing sheet with id=AA3, first strand: chain 'B' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 34 through 40 current: chain 'B' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 through 74 current: chain 'B' and resid 90 through 99 Processing sheet with id=AA4, first strand: chain 'B' and resid 128 through 142 removed outlier: 7.111A pdb=" N LEU B 139 " --> pdb=" O GLU B 151 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N GLU B 151 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS B 141 " --> pdb=" O THR B 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 148 through 152 current: chain 'B' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 196 through 201 current: chain 'B' and resid 322 through 323 Processing sheet with id=AA5, first strand: chain 'C' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 34 through 40 current: chain 'C' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 70 through 74 current: chain 'C' and resid 90 through 99 Processing sheet with id=AA6, first strand: chain 'C' and resid 128 through 142 removed outlier: 7.061A pdb=" N LEU C 139 " --> pdb=" O GLU C 151 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU C 151 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS C 141 " --> pdb=" O THR C 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 148 through 152 current: chain 'C' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 196 through 201 current: chain 'C' and resid 322 through 323 Processing sheet with id=AA7, first strand: chain 'F' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 34 through 40 current: chain 'F' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 70 through 74 current: chain 'F' and resid 90 through 99 Processing sheet with id=AA8, first strand: chain 'F' and resid 128 through 142 removed outlier: 5.289A pdb=" N GLU F 151 " --> pdb=" O LYS F 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 148 through 152 current: chain 'F' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 196 through 201 current: chain 'F' and resid 322 through 323 Processing sheet with id=AA9, first strand: chain 'G' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 34 through 40 current: chain 'G' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 70 through 74 current: chain 'G' and resid 90 through 99 Processing sheet with id=AB1, first strand: chain 'G' and resid 128 through 142 removed outlier: 7.113A pdb=" N LEU G 139 " --> pdb=" O GLU G 151 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N GLU G 151 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LYS G 141 " --> pdb=" O THR G 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 148 through 152 current: chain 'G' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 196 through 201 current: chain 'G' and resid 322 through 323 Processing sheet with id=AB2, first strand: chain 'H' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 34 through 40 current: chain 'H' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 70 through 74 current: chain 'H' and resid 90 through 99 Processing sheet with id=AB3, first strand: chain 'H' and resid 128 through 142 removed outlier: 5.331A pdb=" N GLU H 151 " --> pdb=" O LYS H 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 148 through 152 current: chain 'H' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 196 through 201 current: chain 'H' and resid 322 through 323 Processing sheet with id=AB4, first strand: chain 'L' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 34 through 40 current: chain 'L' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 70 through 74 current: chain 'L' and resid 90 through 99 Processing sheet with id=AB5, first strand: chain 'L' and resid 128 through 142 removed outlier: 5.281A pdb=" N GLU L 151 " --> pdb=" O LYS L 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 148 through 152 current: chain 'L' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 196 through 201 current: chain 'L' and resid 322 through 323 Processing sheet with id=AB6, first strand: chain 'N' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 34 through 40 current: chain 'N' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 70 through 74 current: chain 'N' and resid 90 through 99 Processing sheet with id=AB7, first strand: chain 'N' and resid 128 through 142 removed outlier: 7.109A pdb=" N LEU N 139 " --> pdb=" O GLU N 151 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU N 151 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N LYS N 141 " --> pdb=" O THR N 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 148 through 152 current: chain 'N' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'N' and resid 196 through 201 current: chain 'N' and resid 322 through 323 Processing sheet with id=AB8, first strand: chain 'O' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 34 through 40 current: chain 'O' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 70 through 74 current: chain 'O' and resid 90 through 99 Processing sheet with id=AB9, first strand: chain 'O' and resid 128 through 142 removed outlier: 7.062A pdb=" N LEU O 139 " --> pdb=" O GLU O 151 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N GLU O 151 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N LYS O 141 " --> pdb=" O THR O 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 148 through 152 current: chain 'O' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'O' and resid 196 through 201 current: chain 'O' and resid 322 through 323 Processing sheet with id=AC1, first strand: chain 'R' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 34 through 40 current: chain 'R' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 70 through 74 current: chain 'R' and resid 90 through 99 Processing sheet with id=AC2, first strand: chain 'R' and resid 128 through 142 removed outlier: 5.271A pdb=" N GLU R 151 " --> pdb=" O LYS R 141 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 148 through 152 current: chain 'R' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 196 through 201 current: chain 'R' and resid 322 through 323 Processing sheet with id=AC3, first strand: chain 'S' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 34 through 40 current: chain 'S' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 70 through 74 current: chain 'S' and resid 90 through 99 Processing sheet with id=AC4, first strand: chain 'S' and resid 128 through 142 removed outlier: 7.117A pdb=" N LEU S 139 " --> pdb=" O GLU S 151 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLU S 151 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LYS S 141 " --> pdb=" O THR S 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 148 through 152 current: chain 'S' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'S' and resid 196 through 201 current: chain 'S' and resid 322 through 323 Processing sheet with id=AC5, first strand: chain 'T' and resid 20 through 28 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 34 through 40 current: chain 'T' and resid 70 through 74 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 70 through 74 current: chain 'T' and resid 90 through 99 Processing sheet with id=AC6, first strand: chain 'T' and resid 128 through 142 removed outlier: 7.058A pdb=" N LEU T 139 " --> pdb=" O GLU T 151 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU T 151 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N LYS T 141 " --> pdb=" O THR T 149 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 148 through 152 current: chain 'T' and resid 196 through 201 WARNING: can't find start of bonding for strands! previous: chain 'T' and resid 196 through 201 current: chain 'T' and resid 322 through 323 1545 hydrogen bonds defined for protein. 4413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.86 Time building geometry restraints manager: 19.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.97 - 1.13: 120 1.13 - 1.30: 7452 1.30 - 1.47: 17226 1.47 - 1.64: 19074 1.64 - 1.81: 348 Bond restraints: 44220 Sorted by residual: bond pdb=" NE2 GLN O 503 " pdb="HE21 GLN O 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" NE2 GLN R 503 " pdb="HE21 GLN R 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" NE2 GLN H 503 " pdb="HE21 GLN H 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.09e+01 bond pdb=" NE2 GLN B 503 " pdb="HE21 GLN B 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" NE2 GLN S 503 " pdb="HE21 GLN S 503 " ideal model delta sigma weight residual 0.860 1.016 -0.156 2.00e-02 2.50e+03 6.08e+01 ... (remaining 44215 not shown) Histogram of bond angle deviations from ideal: 100.21 - 106.97: 1428 106.97 - 113.72: 23749 113.72 - 120.48: 17341 120.48 - 127.24: 16955 127.24 - 134.00: 491 Bond angle restraints: 59964 Sorted by residual: angle pdb=" N SER G 57 " pdb=" CA SER G 57 " pdb=" C SER G 57 " ideal model delta sigma weight residual 113.18 109.53 3.65 1.21e+00 6.83e-01 9.08e+00 angle pdb=" CA GLY L 412 " pdb=" C GLY L 412 " pdb=" O GLY L 412 " ideal model delta sigma weight residual 122.24 119.70 2.54 8.70e-01 1.32e+00 8.55e+00 angle pdb=" CA GLY A 412 " pdb=" C GLY A 412 " pdb=" O GLY A 412 " ideal model delta sigma weight residual 122.24 119.71 2.53 8.70e-01 1.32e+00 8.49e+00 angle pdb=" CA GLY R 412 " pdb=" C GLY R 412 " pdb=" O GLY R 412 " ideal model delta sigma weight residual 122.24 119.73 2.51 8.70e-01 1.32e+00 8.33e+00 angle pdb=" CA GLY F 412 " pdb=" C GLY F 412 " pdb=" O GLY F 412 " ideal model delta sigma weight residual 122.24 119.75 2.49 8.70e-01 1.32e+00 8.22e+00 ... (remaining 59959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 23511 18.00 - 36.01: 2137 36.01 - 54.01: 631 54.01 - 72.02: 191 72.02 - 90.02: 62 Dihedral angle restraints: 26532 sinusoidal: 10872 harmonic: 15660 Sorted by residual: dihedral pdb=" CA PRO R 163 " pdb=" C PRO R 163 " pdb=" N THR R 164 " pdb=" CA THR R 164 " ideal model delta harmonic sigma weight residual -180.00 -155.15 -24.85 0 5.00e+00 4.00e-02 2.47e+01 dihedral pdb=" CA PRO H 163 " pdb=" C PRO H 163 " pdb=" N THR H 164 " pdb=" CA THR H 164 " ideal model delta harmonic sigma weight residual 180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA PRO O 163 " pdb=" C PRO O 163 " pdb=" N THR O 164 " pdb=" CA THR O 164 " ideal model delta harmonic sigma weight residual -180.00 -155.52 -24.48 0 5.00e+00 4.00e-02 2.40e+01 ... (remaining 26529 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 3685 0.026 - 0.052: 1553 0.052 - 0.077: 763 0.077 - 0.103: 229 0.103 - 0.129: 214 Chirality restraints: 6444 Sorted by residual: chirality pdb=" CA ILE A 334 " pdb=" N ILE A 334 " pdb=" C ILE A 334 " pdb=" CB ILE A 334 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE L 334 " pdb=" N ILE L 334 " pdb=" C ILE L 334 " pdb=" CB ILE L 334 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA PRO R 293 " pdb=" N PRO R 293 " pdb=" C PRO R 293 " pdb=" CB PRO R 293 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.08e-01 ... (remaining 6441 not shown) Planarity restraints: 7860 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN H 503 " 0.122 2.00e-02 2.50e+03 1.17e-01 2.06e+02 pdb=" CD GLN H 503 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN H 503 " -0.116 2.00e-02 2.50e+03 pdb=" NE2 GLN H 503 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN H 503 " -0.163 2.00e-02 2.50e+03 pdb="HE22 GLN H 503 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN O 503 " -0.122 2.00e-02 2.50e+03 1.17e-01 2.06e+02 pdb=" CD GLN O 503 " 0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN O 503 " 0.116 2.00e-02 2.50e+03 pdb=" NE2 GLN O 503 " 0.001 2.00e-02 2.50e+03 pdb="HE21 GLN O 503 " 0.163 2.00e-02 2.50e+03 pdb="HE22 GLN O 503 " -0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN R 503 " 0.122 2.00e-02 2.50e+03 1.17e-01 2.06e+02 pdb=" CD GLN R 503 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN R 503 " -0.116 2.00e-02 2.50e+03 pdb=" NE2 GLN R 503 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN R 503 " -0.162 2.00e-02 2.50e+03 pdb="HE22 GLN R 503 " 0.166 2.00e-02 2.50e+03 ... (remaining 7857 not shown) Histogram of nonbonded interaction distances: 1.69 - 2.27: 130 2.27 - 2.85: 15352 2.85 - 3.43: 48433 3.43 - 4.02: 88664 4.02 - 4.60: 132220 Nonbonded interactions: 284799 Sorted by model distance: nonbonded pdb=" O GLY G 243 " pdb=" H1 GLN G 503 " model vdw 1.686 1.850 nonbonded pdb=" O GLY O 243 " pdb=" H1 GLN O 503 " model vdw 1.687 1.850 nonbonded pdb=" O GLY N 243 " pdb=" H1 GLN N 503 " model vdw 1.687 1.850 nonbonded pdb=" O GLY S 243 " pdb=" H1 GLN S 503 " model vdw 1.692 1.850 nonbonded pdb=" O GLY B 243 " pdb=" H1 GLN B 503 " model vdw 1.694 1.850 ... (remaining 284794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'R' selection = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'M' selection = chain 'P' selection = chain 'Q' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mg 24 5.21 5 S 204 5.16 5 C 27468 2.51 5 N 7296 2.21 5 O 8160 1.98 5 H 120 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.97 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.120 Extract box with map and model: 17.230 Check model and map are aligned: 0.640 Convert atoms to be neutral: 0.320 Process input model: 105.670 Find NCS groups from input model: 3.130 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:12.570 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 144.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 44100 Z= 0.155 Angle : 0.505 5.756 59700 Z= 0.285 Chirality : 0.040 0.129 6444 Planarity : 0.003 0.034 7860 Dihedral : 16.471 90.021 16416 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.12), residues: 5316 helix: 1.25 (0.11), residues: 2244 sheet: -1.18 (0.16), residues: 924 loop : -0.20 (0.14), residues: 2148 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 985 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 923 time to evaluate : 5.386 Fit side-chains outliers start: 62 outliers final: 32 residues processed: 965 average time/residue: 1.6376 time to fit residues: 1919.5188 Evaluate side-chains 748 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 716 time to evaluate : 4.959 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 23 residues processed: 9 average time/residue: 0.4913 time to fit residues: 14.1509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 445 optimal weight: 0.0170 chunk 400 optimal weight: 2.9990 chunk 222 optimal weight: 0.7980 chunk 136 optimal weight: 0.6980 chunk 269 optimal weight: 0.8980 chunk 213 optimal weight: 4.9990 chunk 413 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 251 optimal weight: 9.9990 chunk 308 optimal weight: 10.0000 chunk 479 optimal weight: 10.0000 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 421 ASN B 36 ASN B 169 ASN B 418 GLN C 228 ASN C 421 ASN F 36 ASN F 421 ASN G 36 ASN G 413 ASN G 418 GLN G 445 GLN H 228 ASN H 421 ASN L 36 ASN L 421 ASN N 36 ASN N 418 GLN O 228 ASN O 421 ASN R 36 ASN R 421 ASN S 36 ASN S 169 ASN S 413 ASN T 228 ASN T 421 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 44100 Z= 0.100 Angle : 0.390 4.353 59700 Z= 0.208 Chirality : 0.038 0.137 6444 Planarity : 0.003 0.029 7860 Dihedral : 4.702 52.785 5868 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer Outliers : 1.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.12), residues: 5316 helix: 1.66 (0.11), residues: 2352 sheet: -1.13 (0.16), residues: 864 loop : -0.08 (0.14), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 840 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 750 time to evaluate : 5.099 Fit side-chains outliers start: 90 outliers final: 40 residues processed: 794 average time/residue: 1.5877 time to fit residues: 1543.3575 Evaluate side-chains 752 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 712 time to evaluate : 4.942 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 21 residues processed: 19 average time/residue: 0.6902 time to fit residues: 26.7873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 266 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 399 optimal weight: 7.9990 chunk 326 optimal weight: 9.9990 chunk 132 optimal weight: 10.0000 chunk 480 optimal weight: 8.9990 chunk 518 optimal weight: 0.9990 chunk 427 optimal weight: 0.0470 chunk 476 optimal weight: 0.3980 chunk 163 optimal weight: 0.0070 chunk 385 optimal weight: 0.4980 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 247 HIS B 36 ASN B 169 ASN B 413 ASN C 36 ASN C 421 ASN F 36 ASN F 247 HIS G 36 ASN G 169 ASN G 247 HIS G 413 ASN H 36 ASN H 421 ASN L 36 ASN L 247 HIS N 36 ASN N 169 ASN N 247 HIS N 413 ASN O 36 ASN O 421 ASN R 36 ASN R 247 HIS S 36 ASN S 169 ASN S 247 HIS S 413 ASN T 36 ASN T 421 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.033 44100 Z= 0.083 Angle : 0.358 4.104 59700 Z= 0.188 Chirality : 0.037 0.135 6444 Planarity : 0.002 0.027 7860 Dihedral : 4.169 44.317 5868 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 1.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.12), residues: 5316 helix: 2.12 (0.11), residues: 2352 sheet: -0.73 (0.17), residues: 888 loop : 0.08 (0.14), residues: 2076 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 759 time to evaluate : 5.557 Fit side-chains outliers start: 70 outliers final: 28 residues processed: 804 average time/residue: 1.5416 time to fit residues: 1526.6836 Evaluate side-chains 766 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 738 time to evaluate : 5.262 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 18 residues processed: 10 average time/residue: 0.9384 time to fit residues: 20.0191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 474 optimal weight: 8.9990 chunk 361 optimal weight: 5.9990 chunk 249 optimal weight: 9.9990 chunk 53 optimal weight: 4.9990 chunk 229 optimal weight: 0.3980 chunk 322 optimal weight: 7.9990 chunk 482 optimal weight: 10.0000 chunk 510 optimal weight: 0.0670 chunk 251 optimal weight: 8.9990 chunk 456 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 overall best weight: 3.6924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN B 169 ASN B 189 HIS B 413 ASN C 36 ASN C 189 HIS C 228 ASN C 421 ASN F 36 ASN F 189 HIS G 36 ASN G 169 ASN G 189 HIS G 413 ASN H 36 ASN H 189 HIS H 421 ASN L 36 ASN L 189 HIS N 36 ASN N 169 ASN N 189 HIS N 413 ASN O 36 ASN O 189 HIS O 228 ASN O 421 ASN R 36 ASN R 169 ASN R 189 HIS S 36 ASN S 169 ASN S 189 HIS S 413 ASN T 36 ASN T 189 HIS T 404 ASN T 421 ASN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 44100 Z= 0.285 Angle : 0.578 6.404 59700 Z= 0.315 Chirality : 0.046 0.168 6444 Planarity : 0.005 0.045 7860 Dihedral : 5.576 57.832 5868 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 3.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.11), residues: 5316 helix: 1.43 (0.11), residues: 2340 sheet: -1.63 (0.16), residues: 744 loop : -0.11 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 886 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 737 time to evaluate : 5.214 Fit side-chains outliers start: 149 outliers final: 42 residues processed: 823 average time/residue: 1.5385 time to fit residues: 1560.6126 Evaluate side-chains 771 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 729 time to evaluate : 5.380 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 33 residues processed: 9 average time/residue: 0.4662 time to fit residues: 14.3514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 425 optimal weight: 8.9990 chunk 289 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 380 optimal weight: 0.3980 chunk 210 optimal weight: 6.9990 chunk 435 optimal weight: 10.0000 chunk 352 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 260 optimal weight: 0.6980 chunk 458 optimal weight: 10.0000 chunk 128 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 421 ASN B 36 ASN B 169 ASN B 228 ASN B 413 ASN C 36 ASN C 421 ASN F 36 ASN F 421 ASN G 36 ASN G 169 ASN G 228 ASN G 413 ASN H 36 ASN H 228 ASN H 421 ASN L 36 ASN L 421 ASN N 36 ASN N 169 ASN N 228 ASN N 413 ASN O 36 ASN O 421 ASN R 36 ASN R 169 ASN R 421 ASN S 36 ASN S 169 ASN S 228 ASN S 413 ASN T 36 ASN T 228 ASN T 421 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 0.2124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 44100 Z= 0.101 Angle : 0.404 4.938 59700 Z= 0.214 Chirality : 0.038 0.136 6444 Planarity : 0.003 0.033 7860 Dihedral : 4.895 52.083 5868 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer Outliers : 2.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.12), residues: 5316 helix: 1.86 (0.11), residues: 2340 sheet: -1.46 (0.16), residues: 744 loop : 0.04 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 748 time to evaluate : 5.165 Fit side-chains outliers start: 97 outliers final: 52 residues processed: 800 average time/residue: 1.6048 time to fit residues: 1574.0818 Evaluate side-chains 785 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 733 time to evaluate : 5.032 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 33 residues processed: 19 average time/residue: 0.7136 time to fit residues: 27.1097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 171 optimal weight: 0.8980 chunk 459 optimal weight: 9.9990 chunk 100 optimal weight: 0.1980 chunk 299 optimal weight: 0.0770 chunk 125 optimal weight: 10.0000 chunk 510 optimal weight: 7.9990 chunk 424 optimal weight: 0.5980 chunk 236 optimal weight: 0.6980 chunk 42 optimal weight: 6.9990 chunk 168 optimal weight: 0.7980 chunk 268 optimal weight: 8.9990 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN B 169 ASN B 413 ASN C 36 ASN C 421 ASN F 36 ASN G 36 ASN G 169 ASN G 413 ASN H 36 ASN H 421 ASN L 36 ASN N 36 ASN N 169 ASN N 413 ASN O 36 ASN O 421 ASN R 36 ASN S 36 ASN S 169 ASN S 413 ASN T 36 ASN T 421 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.001 0.033 44100 Z= 0.089 Angle : 0.376 4.801 59700 Z= 0.198 Chirality : 0.038 0.133 6444 Planarity : 0.002 0.029 7860 Dihedral : 4.399 45.249 5868 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.12), residues: 5316 helix: 2.10 (0.11), residues: 2352 sheet: -1.32 (0.16), residues: 744 loop : 0.14 (0.13), residues: 2220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 828 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 749 time to evaluate : 5.596 Fit side-chains outliers start: 79 outliers final: 46 residues processed: 797 average time/residue: 1.6067 time to fit residues: 1584.9034 Evaluate side-chains 784 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 738 time to evaluate : 5.047 Switching outliers to nearest non-outliers outliers start: 46 outliers final: 32 residues processed: 14 average time/residue: 0.4754 time to fit residues: 18.3669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 492 optimal weight: 6.9990 chunk 57 optimal weight: 7.9990 chunk 291 optimal weight: 8.9990 chunk 373 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 430 optimal weight: 7.9990 chunk 285 optimal weight: 1.9990 chunk 508 optimal weight: 10.0000 chunk 318 optimal weight: 0.9980 chunk 310 optimal weight: 0.8980 chunk 234 optimal weight: 9.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 189 HIS B 36 ASN B 169 ASN B 413 ASN C 36 ASN C 421 ASN F 36 ASN G 36 ASN G 169 ASN G 413 ASN H 36 ASN H 421 ASN L 36 ASN N 36 ASN N 169 ASN N 413 ASN N 445 GLN O 36 ASN O 421 ASN R 36 ASN S 36 ASN S 169 ASN S 413 ASN T 36 ASN T 421 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 44100 Z= 0.250 Angle : 0.545 6.307 59700 Z= 0.295 Chirality : 0.044 0.159 6444 Planarity : 0.004 0.042 7860 Dihedral : 5.437 54.980 5868 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer Outliers : 2.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.11), residues: 5316 helix: 1.51 (0.11), residues: 2340 sheet: -1.52 (0.16), residues: 744 loop : 0.01 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 836 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 725 time to evaluate : 5.085 Fit side-chains outliers start: 111 outliers final: 52 residues processed: 790 average time/residue: 1.5483 time to fit residues: 1505.4069 Evaluate side-chains 770 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 718 time to evaluate : 5.061 Switching outliers to nearest non-outliers outliers start: 52 outliers final: 33 residues processed: 19 average time/residue: 0.4980 time to fit residues: 22.8874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 314 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 303 optimal weight: 9.9990 chunk 153 optimal weight: 1.9990 chunk 99 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 323 optimal weight: 0.9990 chunk 346 optimal weight: 7.9990 chunk 251 optimal weight: 4.9990 chunk 47 optimal weight: 6.9990 chunk 400 optimal weight: 7.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN B 169 ASN B 228 ASN B 413 ASN B 445 GLN C 36 ASN C 421 ASN F 36 ASN G 36 ASN G 169 ASN G 228 ASN G 413 ASN H 36 ASN H 421 ASN L 36 ASN N 36 ASN N 169 ASN N 228 ASN N 413 ASN O 36 ASN O 421 ASN R 36 ASN S 36 ASN S 169 ASN S 228 ASN S 413 ASN T 36 ASN T 421 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 44100 Z= 0.190 Angle : 0.491 5.768 59700 Z= 0.266 Chirality : 0.042 0.149 6444 Planarity : 0.003 0.033 7860 Dihedral : 5.347 53.137 5868 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.11), residues: 5316 helix: 1.51 (0.11), residues: 2340 sheet: -1.53 (0.16), residues: 744 loop : -0.01 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 796 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 708 time to evaluate : 5.149 Fit side-chains outliers start: 88 outliers final: 54 residues processed: 757 average time/residue: 1.6049 time to fit residues: 1500.4072 Evaluate side-chains 755 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 701 time to evaluate : 5.011 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 35 residues processed: 19 average time/residue: 0.8361 time to fit residues: 29.6608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 462 optimal weight: 10.0000 chunk 487 optimal weight: 10.0000 chunk 444 optimal weight: 3.9990 chunk 474 optimal weight: 0.0870 chunk 285 optimal weight: 2.9990 chunk 206 optimal weight: 10.0000 chunk 372 optimal weight: 3.9990 chunk 145 optimal weight: 0.0770 chunk 428 optimal weight: 5.9990 chunk 448 optimal weight: 6.9990 chunk 472 optimal weight: 10.0000 overall best weight: 2.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN B 169 ASN B 413 ASN C 36 ASN C 421 ASN F 36 ASN G 36 ASN G 169 ASN G 413 ASN H 36 ASN H 421 ASN L 36 ASN N 36 ASN N 169 ASN N 413 ASN O 36 ASN O 421 ASN R 36 ASN S 36 ASN S 169 ASN S 413 ASN T 36 ASN T 421 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.2385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 44100 Z= 0.188 Angle : 0.495 6.043 59700 Z= 0.267 Chirality : 0.042 0.152 6444 Planarity : 0.004 0.035 7860 Dihedral : 5.350 53.036 5868 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer Outliers : 1.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.11), residues: 5316 helix: 1.50 (0.11), residues: 2340 sheet: -1.53 (0.16), residues: 744 loop : -0.01 (0.13), residues: 2232 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 705 time to evaluate : 5.312 Fit side-chains outliers start: 76 outliers final: 48 residues processed: 756 average time/residue: 1.6385 time to fit residues: 1522.3797 Evaluate side-chains 750 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 702 time to evaluate : 5.293 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 35 residues processed: 13 average time/residue: 0.4998 time to fit residues: 18.3287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 311 optimal weight: 8.9990 chunk 501 optimal weight: 6.9990 chunk 306 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 348 optimal weight: 5.9990 chunk 526 optimal weight: 10.0000 chunk 484 optimal weight: 4.9990 chunk 418 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 323 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN B 36 ASN B 169 ASN B 413 ASN C 36 ASN C 169 ASN C 421 ASN F 36 ASN F 169 ASN G 36 ASN G 169 ASN G 413 ASN H 36 ASN H 169 ASN H 421 ASN L 36 ASN L 169 ASN N 36 ASN N 169 ASN N 413 ASN O 36 ASN O 169 ASN O 421 ASN R 36 ASN R 169 ASN S 36 ASN S 169 ASN S 413 ASN T 36 ASN T 169 ASN T 421 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 44100 Z= 0.330 Angle : 0.626 7.206 59700 Z= 0.341 Chirality : 0.048 0.168 6444 Planarity : 0.005 0.051 7860 Dihedral : 5.816 56.097 5868 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 10.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.11), residues: 5316 helix: 1.17 (0.11), residues: 2316 sheet: -1.64 (0.15), residues: 744 loop : -0.23 (0.13), residues: 2256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10632 Ramachandran restraints generated. 5316 Oldfield, 0 Emsley, 5316 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 763 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 696 time to evaluate : 5.430 Fit side-chains outliers start: 67 outliers final: 40 residues processed: 752 average time/residue: 1.6072 time to fit residues: 1490.0179 Evaluate side-chains 733 residues out of total 4716 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 693 time to evaluate : 4.769 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 38 residues processed: 2 average time/residue: 1.1636 time to fit residues: 9.6103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 528 random chunks: chunk 332 optimal weight: 7.9990 chunk 446 optimal weight: 7.9990 chunk 128 optimal weight: 5.9990 chunk 386 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 9.9990 chunk 419 optimal weight: 8.9990 chunk 175 optimal weight: 2.9990 chunk 430 optimal weight: 0.0570 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 overall best weight: 3.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 421 ASN B 36 ASN B 169 ASN B 413 ASN C 36 ASN ** C 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 421 ASN F 36 ASN F 169 ASN F 421 ASN G 36 ASN G 169 ASN G 413 ASN H 36 ASN H 169 ASN H 228 ASN H 421 ASN L 36 ASN L 421 ASN N 36 ASN N 169 ASN N 413 ASN O 36 ASN O 169 ASN O 421 ASN R 36 ASN R 421 ASN S 36 ASN S 169 ASN S 413 ASN T 36 ASN T 169 ASN T 228 ASN T 421 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.151972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.131778 restraints weight = 39026.294| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.00 r_work: 0.3393 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3733 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3733 r_free = 0.3733 target_work(ls_wunit_k1) = 0.152 | | occupancies: max = 1.00 min = 0.68 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3733 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 44100 Z= 0.263 Angle : 0.562 6.239 59700 Z= 0.306 Chirality : 0.045 0.158 6444 Planarity : 0.004 0.041 7860 Dihedral : 5.698 54.438 5868 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer Outliers : 1.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.11), residues: 5316 helix: 1.24 (0.11), residues: 2328 sheet: -1.66 (0.15), residues: 744 loop : -0.13 (0.13), residues: 2244 =============================================================================== Job complete usr+sys time: 21174.41 seconds wall clock time: 372 minutes 20.41 seconds (22340.41 seconds total)