Starting phenix.real_space_refine on Sat Mar 7 04:24:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rwg_54328/03_2026/9rwg_54328.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rwg_54328/03_2026/9rwg_54328.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rwg_54328/03_2026/9rwg_54328.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rwg_54328/03_2026/9rwg_54328.map" model { file = "/net/cci-nas-00/data/ceres_data/9rwg_54328/03_2026/9rwg_54328.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rwg_54328/03_2026/9rwg_54328.cif" } resolution = 2.19 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 24 5.49 5 Mg 10 5.21 5 S 127 5.16 5 C 23201 2.51 5 N 6427 2.21 5 O 7172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 198 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36961 Number of models: 1 Model: "" Number of chains: 32 Chain: "A" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1625 Classifications: {'peptide': 202} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 190} Chain breaks: 6 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 112 Classifications: {'peptide': 15} Link IDs: {'TRANS': 14} Chain breaks: 3 Chain: "E" Number of atoms: 287 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 287 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 2, 'TRANS': 36} Chain breaks: 5 Chain: "F" Number of atoms: 3515 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3515 Classifications: {'peptide': 438} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 407} Chain breaks: 4 Chain: "G" Number of atoms: 3486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3486 Classifications: {'peptide': 434} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 403} Chain breaks: 4 Chain: "H" Number of atoms: 1477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1477 Classifications: {'peptide': 184} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 174} Chain breaks: 5 Chain: "I" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 199 Classifications: {'peptide': 27} Link IDs: {'PTRANS': 2, 'TRANS': 24} Chain breaks: 4 Chain: "Q" Number of atoms: 1571 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1571 Classifications: {'peptide': 195} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 184} Chain breaks: 5 Chain: "R" Number of atoms: 3490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3490 Classifications: {'peptide': 435} Link IDs: {'PCIS': 1, 'PTRANS': 29, 'TRANS': 404} Chain breaks: 4 Chain: "S" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 144 Classifications: {'peptide': 20} Link IDs: {'PTRANS': 1, 'TRANS': 18} Chain breaks: 3 Chain: "U" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1445 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 170} Chain breaks: 5 Chain: "V" Number of atoms: 3436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3436 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 397} Chain breaks: 4 Chain: "W" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 426, 3429 Classifications: {'peptide': 426} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 397} Chain breaks: 4 Chain: "X" Number of atoms: 1446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1446 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 170} Chain breaks: 5 Chain: "Y" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 105 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain breaks: 3 Chain: "a" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain: "b" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain: "c" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain: "d" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain: "e" Number of atoms: 2172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2172 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 9, 'TRANS': 263} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "e" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 8.10, per 1000 atoms: 0.22 Number of scatterers: 36961 At special positions: 0 Unit cell: (157.339, 134.995, 174.097, 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 127 16.00 P 24 15.00 Mg 10 11.99 O 7172 8.00 N 6427 7.00 C 23201 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.07 Conformation dependent library (CDL) restraints added in 1.5 seconds 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8508 Finding SS restraints... Secondary structure from input PDB file: 124 helices and 87 sheets defined 22.2% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 298 through 304 Processing helix chain 'A' and resid 469 through 473 removed outlier: 4.052A pdb=" N MET A 473 " --> pdb=" O PRO A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 498 Processing helix chain 'A' and resid 565 through 569 removed outlier: 3.714A pdb=" N ILE A 568 " --> pdb=" O GLU A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 4.052A pdb=" N TYR A 708 " --> pdb=" O SER A 705 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 257 Processing helix chain 'F' and resid 270 through 274 removed outlier: 3.795A pdb=" N THR F 274 " --> pdb=" O ASN F 271 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 293 Processing helix chain 'F' and resid 295 through 305 Processing helix chain 'F' and resid 397 through 401 Processing helix chain 'F' and resid 494 through 498 Processing helix chain 'F' and resid 556 through 558 No H-bonds generated for 'chain 'F' and resid 556 through 558' Processing helix chain 'F' and resid 565 through 569 Processing helix chain 'F' and resid 704 through 708 removed outlier: 3.592A pdb=" N TYR F 707 " --> pdb=" O THR F 704 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N TYR F 708 " --> pdb=" O SER F 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 704 through 708' Processing helix chain 'G' and resid 253 through 257 Processing helix chain 'G' and resid 270 through 274 removed outlier: 3.743A pdb=" N THR G 274 " --> pdb=" O ASN G 271 " (cutoff:3.500A) Processing helix chain 'G' and resid 289 through 293 Processing helix chain 'G' and resid 295 through 305 Processing helix chain 'G' and resid 397 through 401 Processing helix chain 'G' and resid 494 through 498 Processing helix chain 'G' and resid 556 through 558 No H-bonds generated for 'chain 'G' and resid 556 through 558' Processing helix chain 'G' and resid 565 through 569 Processing helix chain 'G' and resid 704 through 708 removed outlier: 4.068A pdb=" N TYR G 708 " --> pdb=" O SER G 705 " (cutoff:3.500A) Processing helix chain 'H' and resid 301 through 305 removed outlier: 3.579A pdb=" N ASN H 305 " --> pdb=" O ARG H 301 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 301 through 305' Processing helix chain 'H' and resid 494 through 498 Processing helix chain 'H' and resid 565 through 569 Processing helix chain 'Q' and resid 300 through 304 Processing helix chain 'Q' and resid 494 through 498 Processing helix chain 'Q' and resid 565 through 569 Processing helix chain 'R' and resid 253 through 257 Processing helix chain 'R' and resid 270 through 274 removed outlier: 3.696A pdb=" N THR R 274 " --> pdb=" O ASN R 271 " (cutoff:3.500A) Processing helix chain 'R' and resid 289 through 293 Processing helix chain 'R' and resid 295 through 305 Processing helix chain 'R' and resid 397 through 401 Processing helix chain 'R' and resid 494 through 498 Processing helix chain 'R' and resid 556 through 558 No H-bonds generated for 'chain 'R' and resid 556 through 558' Processing helix chain 'R' and resid 565 through 569 Processing helix chain 'R' and resid 704 through 708 removed outlier: 3.802A pdb=" N TYR R 708 " --> pdb=" O SER R 705 " (cutoff:3.500A) Processing helix chain 'U' and resid 301 through 305 Processing helix chain 'U' and resid 494 through 498 Processing helix chain 'U' and resid 565 through 569 Processing helix chain 'U' and resid 704 through 708 removed outlier: 3.738A pdb=" N TYR U 708 " --> pdb=" O SER U 705 " (cutoff:3.500A) Processing helix chain 'V' and resid 253 through 257 Processing helix chain 'V' and resid 270 through 274 removed outlier: 3.902A pdb=" N THR V 274 " --> pdb=" O ASN V 271 " (cutoff:3.500A) Processing helix chain 'V' and resid 289 through 293 Processing helix chain 'V' and resid 295 through 305 Processing helix chain 'V' and resid 397 through 401 Processing helix chain 'V' and resid 494 through 498 Processing helix chain 'V' and resid 565 through 571 removed outlier: 4.484A pdb=" N THR V 570 " --> pdb=" O GLU V 567 " (cutoff:3.500A) Processing helix chain 'W' and resid 253 through 257 Processing helix chain 'W' and resid 270 through 274 removed outlier: 3.702A pdb=" N THR W 274 " --> pdb=" O ASN W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 289 through 293 Processing helix chain 'W' and resid 295 through 305 Processing helix chain 'W' and resid 397 through 401 Processing helix chain 'W' and resid 494 through 498 Processing helix chain 'W' and resid 556 through 558 No H-bonds generated for 'chain 'W' and resid 556 through 558' Processing helix chain 'W' and resid 565 through 569 Processing helix chain 'X' and resid 301 through 306 Processing helix chain 'X' and resid 565 through 571 removed outlier: 4.347A pdb=" N THR X 570 " --> pdb=" O GLU X 567 " (cutoff:3.500A) Processing helix chain 'X' and resid 704 through 708 removed outlier: 3.738A pdb=" N TYR X 708 " --> pdb=" O SER X 705 " (cutoff:3.500A) Processing helix chain 'a' and resid 19 through 35 Processing helix chain 'a' and resid 38 through 46 Processing helix chain 'a' and resid 46 through 56 removed outlier: 4.160A pdb=" N ALA a 56 " --> pdb=" O SER a 52 " (cutoff:3.500A) Processing helix chain 'a' and resid 56 through 77 removed outlier: 4.004A pdb=" N SER a 61 " --> pdb=" O SER a 57 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS a 64 " --> pdb=" O ARG a 60 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA a 65 " --> pdb=" O SER a 61 " (cutoff:3.500A) Processing helix chain 'a' and resid 79 through 85 removed outlier: 4.158A pdb=" N TYR a 83 " --> pdb=" O THR a 79 " (cutoff:3.500A) Processing helix chain 'a' and resid 96 through 105 removed outlier: 3.546A pdb=" N ASN a 105 " --> pdb=" O ILE a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 108 through 121 Processing helix chain 'a' and resid 139 through 151 removed outlier: 3.801A pdb=" N VAL a 151 " --> pdb=" O ILE a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 166 through 170 removed outlier: 4.173A pdb=" N VAL a 170 " --> pdb=" O ASN a 167 " (cutoff:3.500A) Processing helix chain 'a' and resid 186 through 195 removed outlier: 3.681A pdb=" N ALA a 192 " --> pdb=" O GLU a 188 " (cutoff:3.500A) Processing helix chain 'a' and resid 237 through 243 Processing helix chain 'a' and resid 255 through 259 Processing helix chain 'a' and resid 262 through 276 Processing helix chain 'b' and resid 20 through 35 removed outlier: 4.493A pdb=" N GLU b 26 " --> pdb=" O ALA b 22 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU b 27 " --> pdb=" O ARG b 23 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 46 Processing helix chain 'b' and resid 46 through 54 Processing helix chain 'b' and resid 56 through 77 Processing helix chain 'b' and resid 80 through 85 Processing helix chain 'b' and resid 96 through 105 removed outlier: 3.724A pdb=" N ASN b 105 " --> pdb=" O ILE b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 108 through 122 Processing helix chain 'b' and resid 138 through 151 removed outlier: 4.441A pdb=" N ASN b 142 " --> pdb=" O THR b 138 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA b 144 " --> pdb=" O LYS b 140 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLU b 145 " --> pdb=" O THR b 141 " (cutoff:3.500A) Processing helix chain 'b' and resid 186 through 195 Processing helix chain 'b' and resid 237 through 243 Processing helix chain 'b' and resid 255 through 259 Processing helix chain 'b' and resid 262 through 276 Processing helix chain 'c' and resid 19 through 23 Processing helix chain 'c' and resid 24 through 32 removed outlier: 4.054A pdb=" N TRP c 30 " --> pdb=" O GLU c 26 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL c 32 " --> pdb=" O VAL c 28 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 55 removed outlier: 3.911A pdb=" N TRP c 42 " --> pdb=" O SER c 38 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU c 45 " --> pdb=" O GLN c 41 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N GLN c 47 " --> pdb=" O ILE c 43 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N ALA c 48 " --> pdb=" O GLN c 44 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N SER c 49 " --> pdb=" O GLU c 45 " (cutoff:3.500A) Processing helix chain 'c' and resid 56 through 62 Processing helix chain 'c' and resid 63 through 65 No H-bonds generated for 'chain 'c' and resid 63 through 65' Processing helix chain 'c' and resid 66 through 78 removed outlier: 3.963A pdb=" N ALA c 70 " --> pdb=" O ALA c 66 " (cutoff:3.500A) Processing helix chain 'c' and resid 79 through 85 removed outlier: 4.085A pdb=" N TYR c 83 " --> pdb=" O THR c 79 " (cutoff:3.500A) Processing helix chain 'c' and resid 96 through 105 Processing helix chain 'c' and resid 108 through 122 Processing helix chain 'c' and resid 139 through 151 removed outlier: 3.597A pdb=" N VAL c 151 " --> pdb=" O ILE c 147 " (cutoff:3.500A) Processing helix chain 'c' and resid 186 through 195 Processing helix chain 'c' and resid 237 through 243 Processing helix chain 'c' and resid 255 through 259 removed outlier: 4.397A pdb=" N GLY c 259 " --> pdb=" O HIS c 256 " (cutoff:3.500A) Processing helix chain 'c' and resid 262 through 276 Processing helix chain 'd' and resid 19 through 23 removed outlier: 4.201A pdb=" N ARG d 23 " --> pdb=" O LYS d 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 19 through 23' Processing helix chain 'd' and resid 23 through 28 Processing helix chain 'd' and resid 28 through 33 Processing helix chain 'd' and resid 38 through 46 removed outlier: 3.875A pdb=" N GLN d 44 " --> pdb=" O LYS d 40 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU d 45 " --> pdb=" O GLN d 41 " (cutoff:3.500A) Processing helix chain 'd' and resid 46 through 53 Processing helix chain 'd' and resid 59 through 78 removed outlier: 4.436A pdb=" N ILE d 63 " --> pdb=" O SER d 59 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LEU d 67 " --> pdb=" O ILE d 63 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ASP d 68 " --> pdb=" O LYS d 64 " (cutoff:3.500A) Processing helix chain 'd' and resid 80 through 85 Processing helix chain 'd' and resid 92 through 95 Processing helix chain 'd' and resid 96 through 106 Processing helix chain 'd' and resid 108 through 121 removed outlier: 3.717A pdb=" N SER d 114 " --> pdb=" O GLN d 110 " (cutoff:3.500A) Processing helix chain 'd' and resid 138 through 151 removed outlier: 4.169A pdb=" N ASN d 142 " --> pdb=" O THR d 138 " (cutoff:3.500A) Processing helix chain 'd' and resid 186 through 195 Processing helix chain 'd' and resid 237 through 243 Processing helix chain 'd' and resid 264 through 276 removed outlier: 3.536A pdb=" N ASP d 268 " --> pdb=" O GLN d 264 " (cutoff:3.500A) Processing helix chain 'e' and resid 20 through 35 removed outlier: 3.581A pdb=" N GLU e 26 " --> pdb=" O ALA e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 38 through 46 removed outlier: 3.516A pdb=" N GLN e 44 " --> pdb=" O LYS e 40 " (cutoff:3.500A) Processing helix chain 'e' and resid 46 through 54 Processing helix chain 'e' and resid 56 through 77 Processing helix chain 'e' and resid 79 through 85 removed outlier: 3.711A pdb=" N TYR e 83 " --> pdb=" O THR e 79 " (cutoff:3.500A) Processing helix chain 'e' and resid 96 through 105 removed outlier: 3.510A pdb=" N ASN e 105 " --> pdb=" O ILE e 101 " (cutoff:3.500A) Processing helix chain 'e' and resid 108 through 122 Processing helix chain 'e' and resid 139 through 151 removed outlier: 3.654A pdb=" N VAL e 151 " --> pdb=" O ILE e 147 " (cutoff:3.500A) Processing helix chain 'e' and resid 186 through 195 Processing helix chain 'e' and resid 237 through 243 Processing helix chain 'e' and resid 262 through 276 Processing sheet with id=AA1, first strand: chain 'A' and resid 424 through 425 removed outlier: 3.637A pdb=" N PHE A 309 " --> pdb=" O HIS A 424 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N GLN A 690 " --> pdb=" O TRP A 307 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 427 through 429 Processing sheet with id=AA3, first strand: chain 'A' and resid 446 through 452 removed outlier: 6.769A pdb=" N GLY A 464 " --> pdb=" O SER A 449 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N THR A 451 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 485 through 486 Processing sheet with id=AA5, first strand: chain 'A' and resid 490 through 492 Processing sheet with id=AA6, first strand: chain 'A' and resid 595 through 598 removed outlier: 3.819A pdb=" N GLY A 580 " --> pdb=" O VAL A 598 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 608 through 609 Processing sheet with id=AA8, first strand: chain 'E' and resid 629 through 630 Processing sheet with id=AA9, first strand: chain 'F' and resid 228 through 229 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 228 through 229 current: chain 'G' and resid 275 through 285 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 232 through 236 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 239 through 250 current: chain 'F' and resid 332 through 337 Processing sheet with id=AB2, first strand: chain 'F' and resid 259 through 263 Processing sheet with id=AB3, first strand: chain 'F' and resid 384 through 385 Processing sheet with id=AB4, first strand: chain 'F' and resid 427 through 429 Processing sheet with id=AB5, first strand: chain 'F' and resid 485 through 486 Processing sheet with id=AB6, first strand: chain 'F' and resid 490 through 492 Processing sheet with id=AB7, first strand: chain 'F' and resid 516 through 519 removed outlier: 3.915A pdb=" N GLY Q 580 " --> pdb=" O VAL Q 598 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 544 through 546 Processing sheet with id=AB9, first strand: chain 'F' and resid 621 through 623 removed outlier: 6.132A pdb=" N ALA F 622 " --> pdb=" O LEU F 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'F' and resid 629 through 630 removed outlier: 6.352A pdb=" N LEU Q 481 " --> pdb=" O VAL Q 608 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 672 through 673 Processing sheet with id=AC3, first strand: chain 'G' and resid 228 through 229 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 228 through 229 current: chain 'W' and resid 275 through 285 No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'G' and resid 233 through 236 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 239 through 250 current: chain 'G' and resid 332 through 338 Processing sheet with id=AC5, first strand: chain 'G' and resid 384 through 385 Processing sheet with id=AC6, first strand: chain 'G' and resid 427 through 429 Processing sheet with id=AC7, first strand: chain 'G' and resid 485 through 486 Processing sheet with id=AC8, first strand: chain 'G' and resid 490 through 492 Processing sheet with id=AC9, first strand: chain 'G' and resid 544 through 546 Processing sheet with id=AD1, first strand: chain 'G' and resid 621 through 623 removed outlier: 6.285A pdb=" N ALA G 622 " --> pdb=" O LEU G 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'G' and resid 672 through 673 Processing sheet with id=AD3, first strand: chain 'H' and resid 306 through 308 removed outlier: 6.419A pdb=" N GLN H 690 " --> pdb=" O TRP H 307 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'H' and resid 427 through 429 Processing sheet with id=AD5, first strand: chain 'H' and resid 446 through 452 removed outlier: 6.692A pdb=" N GLY H 464 " --> pdb=" O SER H 449 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N THR H 451 " --> pdb=" O THR H 462 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 485 through 486 Processing sheet with id=AD7, first strand: chain 'H' and resid 491 through 492 Processing sheet with id=AD8, first strand: chain 'H' and resid 595 through 598 removed outlier: 3.936A pdb=" N GLY H 580 " --> pdb=" O VAL H 598 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 608 through 609 Processing sheet with id=AE1, first strand: chain 'Q' and resid 427 through 429 Processing sheet with id=AE2, first strand: chain 'Q' and resid 446 through 452 removed outlier: 6.873A pdb=" N GLY Q 464 " --> pdb=" O SER Q 449 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR Q 451 " --> pdb=" O THR Q 462 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 485 through 486 Processing sheet with id=AE4, first strand: chain 'Q' and resid 490 through 492 Processing sheet with id=AE5, first strand: chain 'R' and resid 232 through 236 WARNING: can't find start of bonding for strands! previous: chain 'R' and resid 239 through 250 current: chain 'R' and resid 332 through 337 Processing sheet with id=AE6, first strand: chain 'R' and resid 259 through 263 Processing sheet with id=AE7, first strand: chain 'R' and resid 384 through 385 Processing sheet with id=AE8, first strand: chain 'R' and resid 427 through 429 Processing sheet with id=AE9, first strand: chain 'R' and resid 485 through 486 Processing sheet with id=AF1, first strand: chain 'R' and resid 490 through 492 Processing sheet with id=AF2, first strand: chain 'R' and resid 517 through 519 removed outlier: 3.734A pdb=" N GLY U 580 " --> pdb=" O VAL U 598 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'R' and resid 544 through 546 Processing sheet with id=AF4, first strand: chain 'R' and resid 621 through 623 removed outlier: 6.233A pdb=" N ALA R 622 " --> pdb=" O LEU R 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF4 Processing sheet with id=AF5, first strand: chain 'R' and resid 629 through 631 removed outlier: 3.965A pdb=" N MET U 607 " --> pdb=" O PHE R 631 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'R' and resid 672 through 673 Processing sheet with id=AF7, first strand: chain 'U' and resid 306 through 308 removed outlier: 6.466A pdb=" N GLN U 690 " --> pdb=" O TRP U 307 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'U' and resid 427 through 429 Processing sheet with id=AF9, first strand: chain 'U' and resid 446 through 452 removed outlier: 5.574A pdb=" N LEU U 448 " --> pdb=" O SER U 466 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N SER U 466 " --> pdb=" O LEU U 448 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLN U 452 " --> pdb=" O THR U 462 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N THR U 462 " --> pdb=" O GLN U 452 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'U' and resid 485 through 486 Processing sheet with id=AG2, first strand: chain 'U' and resid 491 through 492 Processing sheet with id=AG3, first strand: chain 'V' and resid 232 through 236 WARNING: can't find start of bonding for strands! previous: chain 'V' and resid 239 through 250 current: chain 'V' and resid 332 through 337 Processing sheet with id=AG4, first strand: chain 'V' and resid 259 through 263 Processing sheet with id=AG5, first strand: chain 'V' and resid 384 through 385 removed outlier: 3.551A pdb=" N GLN V 388 " --> pdb=" O ASN V 385 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'V' and resid 485 through 486 Processing sheet with id=AG7, first strand: chain 'V' and resid 490 through 492 Processing sheet with id=AG8, first strand: chain 'V' and resid 516 through 519 removed outlier: 3.986A pdb=" N GLY X 580 " --> pdb=" O VAL X 598 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'V' and resid 544 through 546 Processing sheet with id=AH1, first strand: chain 'V' and resid 555 through 556 removed outlier: 5.739A pdb=" N THR X 462 " --> pdb=" O GLN X 452 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLN X 452 " --> pdb=" O THR X 462 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N SER X 466 " --> pdb=" O LEU X 448 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU X 448 " --> pdb=" O SER X 466 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'V' and resid 621 through 623 removed outlier: 6.117A pdb=" N ALA V 622 " --> pdb=" O LEU V 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'V' and resid 629 through 630 Processing sheet with id=AH4, first strand: chain 'V' and resid 672 through 673 Processing sheet with id=AH5, first strand: chain 'W' and resid 232 through 236 WARNING: can't find start of bonding for strands! previous: chain 'W' and resid 239 through 250 current: chain 'W' and resid 332 through 337 Processing sheet with id=AH6, first strand: chain 'W' and resid 384 through 385 Processing sheet with id=AH7, first strand: chain 'W' and resid 485 through 486 Processing sheet with id=AH8, first strand: chain 'W' and resid 490 through 492 Processing sheet with id=AH9, first strand: chain 'W' and resid 544 through 546 Processing sheet with id=AI1, first strand: chain 'W' and resid 621 through 623 removed outlier: 6.149A pdb=" N ALA W 622 " --> pdb=" O LEU W 642 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI1 Processing sheet with id=AI2, first strand: chain 'W' and resid 671 through 673 removed outlier: 3.520A pdb=" N VAL a 227 " --> pdb=" O THR a 234 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'X' and resid 427 through 429 Processing sheet with id=AI4, first strand: chain 'X' and resid 485 through 486 Processing sheet with id=AI5, first strand: chain 'X' and resid 491 through 492 Processing sheet with id=AI6, first strand: chain 'a' and resid 155 through 156 removed outlier: 6.452A pdb=" N GLY a 155 " --> pdb=" O TRP a 176 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N GLU a 178 " --> pdb=" O GLY a 155 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ILE a 175 " --> pdb=" O ILE a 217 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N THR a 219 " --> pdb=" O ILE a 175 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N TRP a 177 " --> pdb=" O THR a 219 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ILE a 130 " --> pdb=" O VAL a 218 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N SER a 220 " --> pdb=" O ILE a 130 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU a 132 " --> pdb=" O SER a 220 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N THR a 129 " --> pdb=" O PHE a 246 " (cutoff:3.500A) removed outlier: 8.184A pdb=" N PHE a 248 " --> pdb=" O THR a 129 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TRP a 131 " --> pdb=" O PHE a 248 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'a' and resid 199 through 201 Processing sheet with id=AI8, first strand: chain 'b' and resid 154 through 156 removed outlier: 6.224A pdb=" N GLY b 155 " --> pdb=" O TRP b 176 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE b 130 " --> pdb=" O VAL b 218 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N SER b 220 " --> pdb=" O ILE b 130 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU b 132 " --> pdb=" O SER b 220 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'b' and resid 199 through 201 Processing sheet with id=AJ1, first strand: chain 'c' and resid 155 through 156 removed outlier: 6.591A pdb=" N GLY c 155 " --> pdb=" O TRP c 176 " (cutoff:3.500A) removed outlier: 7.715A pdb=" N GLU c 178 " --> pdb=" O GLY c 155 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ILE c 175 " --> pdb=" O ILE c 217 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N THR c 219 " --> pdb=" O ILE c 175 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TRP c 177 " --> pdb=" O THR c 219 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N THR c 129 " --> pdb=" O PHE c 246 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N PHE c 248 " --> pdb=" O THR c 129 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TRP c 131 " --> pdb=" O PHE c 248 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'c' and resid 199 through 201 removed outlier: 3.534A pdb=" N VAL c 199 " --> pdb=" O ILE c 211 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'd' and resid 175 through 177 removed outlier: 6.004A pdb=" N ILE d 175 " --> pdb=" O ILE d 217 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N THR d 219 " --> pdb=" O ILE d 175 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N TRP d 177 " --> pdb=" O THR d 219 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N PHE d 248 " --> pdb=" O THR d 129 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N TRP d 131 " --> pdb=" O PHE d 248 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'd' and resid 199 through 201 Processing sheet with id=AJ5, first strand: chain 'e' and resid 154 through 156 removed outlier: 6.316A pdb=" N GLY e 155 " --> pdb=" O TRP e 176 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N THR e 129 " --> pdb=" O PHE e 246 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N PHE e 248 " --> pdb=" O THR e 129 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N TRP e 131 " --> pdb=" O PHE e 248 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'e' and resid 199 through 201 785 hydrogen bonds defined for protein. 1884 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: 7.20 Time building geometry restraints manager: 4.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10716 1.33 - 1.45: 7591 1.45 - 1.58: 19354 1.58 - 1.70: 33 1.70 - 1.82: 204 Bond restraints: 37898 Sorted by residual: bond pdb=" C4 ADP V2000 " pdb=" C5 ADP V2000 " ideal model delta sigma weight residual 1.490 1.352 0.138 2.00e-02 2.50e+03 4.79e+01 bond pdb=" C4 ADP e1000 " pdb=" C5 ADP e1000 " ideal model delta sigma weight residual 1.490 1.355 0.135 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C5 ADP V2000 " pdb=" C6 ADP V2000 " ideal model delta sigma weight residual 1.490 1.386 0.104 2.00e-02 2.50e+03 2.70e+01 bond pdb=" C5 ADP e1000 " pdb=" C6 ADP e1000 " ideal model delta sigma weight residual 1.490 1.390 0.100 2.00e-02 2.50e+03 2.49e+01 bond pdb=" C8 ADP V2000 " pdb=" N9 ADP V2000 " ideal model delta sigma weight residual 1.337 1.402 -0.065 2.00e-02 2.50e+03 1.05e+01 ... (remaining 37893 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 50862 2.76 - 5.51: 570 5.51 - 8.27: 65 8.27 - 11.03: 5 11.03 - 13.78: 7 Bond angle restraints: 51509 Sorted by residual: angle pdb=" OG1 THR G 327 " pdb=" CB THR G 327 " pdb=" CG2 THR G 327 " ideal model delta sigma weight residual 109.30 120.53 -11.23 2.00e+00 2.50e-01 3.15e+01 angle pdb=" N VAL d 280 " pdb=" CA VAL d 280 " pdb=" C VAL d 280 " ideal model delta sigma weight residual 109.34 120.65 -11.31 2.08e+00 2.31e-01 2.96e+01 angle pdb=" C GLU d 279 " pdb=" N VAL d 280 " pdb=" CA VAL d 280 " ideal model delta sigma weight residual 121.97 130.95 -8.98 1.80e+00 3.09e-01 2.49e+01 angle pdb=" CA THR G 327 " pdb=" CB THR G 327 " pdb=" CG2 THR G 327 " ideal model delta sigma weight residual 110.50 118.68 -8.18 1.70e+00 3.46e-01 2.32e+01 angle pdb=" CA ASP e 255 " pdb=" CB ASP e 255 " pdb=" CG ASP e 255 " ideal model delta sigma weight residual 112.60 117.27 -4.67 1.00e+00 1.00e+00 2.18e+01 ... (remaining 51504 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.74: 21231 29.74 - 59.49: 817 59.49 - 89.23: 123 89.23 - 118.98: 7 118.98 - 148.72: 3 Dihedral angle restraints: 22181 sinusoidal: 8964 harmonic: 13217 Sorted by residual: dihedral pdb=" O2A ADP V2000 " pdb=" O3A ADP V2000 " pdb=" PA ADP V2000 " pdb=" PB ADP V2000 " ideal model delta sinusoidal sigma weight residual 300.00 151.28 148.72 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C5' ADP V2000 " pdb=" O5' ADP V2000 " pdb=" PA ADP V2000 " pdb=" O2A ADP V2000 " ideal model delta sinusoidal sigma weight residual 300.00 151.54 148.46 1 2.00e+01 2.50e-03 4.45e+01 dihedral pdb=" C VAL d 280 " pdb=" N VAL d 280 " pdb=" CA VAL d 280 " pdb=" CB VAL d 280 " ideal model delta harmonic sigma weight residual -122.00 -137.96 15.96 0 2.50e+00 1.60e-01 4.07e+01 ... (remaining 22178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.281: 5431 0.281 - 0.563: 4 0.563 - 0.844: 1 0.844 - 1.126: 0 1.126 - 1.407: 1 Chirality restraints: 5437 Sorted by residual: chirality pdb=" CB THR G 327 " pdb=" CA THR G 327 " pdb=" OG1 THR G 327 " pdb=" CG2 THR G 327 " both_signs ideal model delta sigma weight residual False 2.55 1.14 1.41 2.00e-01 2.50e+01 4.95e+01 chirality pdb=" CA VAL d 280 " pdb=" N VAL d 280 " pdb=" C VAL d 280 " pdb=" CB VAL d 280 " both_signs ideal model delta sigma weight residual False 2.44 1.86 0.58 2.00e-01 2.50e+01 8.30e+00 chirality pdb=" CA THR e 137 " pdb=" N THR e 137 " pdb=" C THR e 137 " pdb=" CB THR e 137 " both_signs ideal model delta sigma weight residual False 2.53 2.13 0.40 2.00e-01 2.50e+01 3.98e+00 ... (remaining 5434 not shown) Planarity restraints: 6683 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' ADP e1000 " -0.126 2.00e-02 2.50e+03 5.29e-02 7.70e+01 pdb=" C2 ADP e1000 " 0.030 2.00e-02 2.50e+03 pdb=" C4 ADP e1000 " 0.027 2.00e-02 2.50e+03 pdb=" C5 ADP e1000 " -0.006 2.00e-02 2.50e+03 pdb=" C6 ADP e1000 " -0.021 2.00e-02 2.50e+03 pdb=" C8 ADP e1000 " 0.079 2.00e-02 2.50e+03 pdb=" N1 ADP e1000 " -0.020 2.00e-02 2.50e+03 pdb=" N3 ADP e1000 " 0.051 2.00e-02 2.50e+03 pdb=" N6 ADP e1000 " -0.053 2.00e-02 2.50e+03 pdb=" N7 ADP e1000 " 0.010 2.00e-02 2.50e+03 pdb=" N9 ADP e1000 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 733 " -0.106 2.00e-02 2.50e+03 5.67e-02 6.43e+01 pdb=" CG TYR V 733 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR V 733 " 0.064 2.00e-02 2.50e+03 pdb=" CD2 TYR V 733 " 0.039 2.00e-02 2.50e+03 pdb=" CE1 TYR V 733 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR V 733 " 0.040 2.00e-02 2.50e+03 pdb=" CZ TYR V 733 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR V 733 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 703 " -0.097 2.00e-02 2.50e+03 5.41e-02 5.86e+01 pdb=" CG TYR V 703 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR V 703 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR V 703 " 0.042 2.00e-02 2.50e+03 pdb=" CE1 TYR V 703 " 0.027 2.00e-02 2.50e+03 pdb=" CE2 TYR V 703 " 0.036 2.00e-02 2.50e+03 pdb=" CZ TYR V 703 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR V 703 " -0.085 2.00e-02 2.50e+03 ... (remaining 6680 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 44 2.44 - 3.06: 24063 3.06 - 3.67: 55243 3.67 - 4.29: 90741 4.29 - 4.90: 144738 Nonbonded interactions: 314829 Sorted by model distance: nonbonded pdb=" O2B ADP W2000 " pdb="MG MG W2001 " model vdw 1.827 2.170 nonbonded pdb=" OE2 GLU W 567 " pdb="MG MG W2001 " model vdw 1.884 2.170 nonbonded pdb=" O2A ADP G2000 " pdb="MG MG G2001 " model vdw 1.889 2.170 nonbonded pdb=" O2A ADP A2000 " pdb="MG MG A2001 " model vdw 1.898 2.170 nonbonded pdb=" O1B ADP V2000 " pdb="MG MG V2001 " model vdw 1.899 2.170 ... (remaining 314824 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 300 through 309 or resid 424 through 498 or resid 525 thro \ ugh 538 or resid 563 through 613 or resid 690 through 708 or resid 729 through 2 \ 001)) selection = (chain 'H' and (resid 300 through 498 or resid 525 through 538 or resid 563 thro \ ugh 613 or resid 690 through 708 or resid 729 through 2001)) selection = (chain 'Q' and (resid 300 through 309 or resid 424 through 498 or resid 525 thro \ ugh 538 or resid 563 through 613 or resid 690 through 708 or resid 729 through 2 \ 001)) selection = (chain 'U' and (resid 300 through 613 or resid 690 through 2001)) selection = (chain 'X' and (resid 300 through 708 or resid 729 through 2001)) } ncs_group { reference = (chain 'B' and resid 391 through 629) selection = chain 'Y' } ncs_group { reference = (chain 'F' and (resid 225 through 429 or resid 483 through 579 or resid 599 thro \ ugh 602 or resid 609 through 692 or resid 700 through 735 or resid 2000 through \ 2001)) selection = (chain 'G' and (resid 225 through 429 or resid 483 through 579 or resid 599 thro \ ugh 602 or resid 609 through 692 or resid 700 through 735 or resid 2000 through \ 2001)) selection = (chain 'R' and (resid 225 through 429 or resid 483 through 579 or resid 599 thro \ ugh 602 or resid 609 through 692 or resid 700 through 735 or resid 2000 through \ 2001)) selection = (chain 'V' and (resid 225 through 692 or resid 700 through 2001)) selection = chain 'W' } ncs_group { reference = chain 'a' selection = chain 'b' selection = (chain 'c' and resid 18 through 290) selection = chain 'd' selection = (chain 'e' and resid 18 through 290) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 0.620 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 32.030 Find NCS groups from input model: 1.180 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 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 : 0.004 0.138 37898 Z= 0.203 Angle : 0.681 13.784 51509 Z= 0.357 Chirality : 0.048 1.407 5437 Planarity : 0.004 0.079 6683 Dihedral : 15.835 148.723 13673 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.90 % Favored : 98.05 % Rotamer: Outliers : 0.95 % Allowed : 13.73 % Favored : 85.32 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.51 (0.12), residues: 4413 helix: 0.32 (0.20), residues: 705 sheet: -0.29 (0.18), residues: 684 loop : -0.48 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG b 253 TYR 0.106 0.002 TYR V 733 PHE 0.040 0.001 PHE d 246 TRP 0.046 0.001 TRP d 119 HIS 0.007 0.001 HIS d 276 Details of bonding type rmsd covalent geometry : bond 0.00420 (37898) covalent geometry : angle 0.68140 (51509) hydrogen bonds : bond 0.18606 ( 785) hydrogen bonds : angle 7.03964 ( 1884) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 433 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 437 MET cc_start: 0.9266 (pmm) cc_final: 0.8956 (pmm) REVERT: A 442 ASP cc_start: 0.8986 (m-30) cc_final: 0.8684 (m-30) REVERT: A 566 GLU cc_start: 0.8547 (pp20) cc_final: 0.8306 (pp20) REVERT: E 586 LEU cc_start: 0.8460 (OUTLIER) cc_final: 0.7997 (mp) REVERT: H 577 GLU cc_start: 0.8527 (mt-10) cc_final: 0.8095 (mm-30) REVERT: H 594 GLN cc_start: 0.8424 (mt0) cc_final: 0.8132 (pt0) REVERT: Q 301 ARG cc_start: 0.9062 (ttm110) cc_final: 0.7728 (mpt180) REVERT: Q 487 ARG cc_start: 0.8712 (OUTLIER) cc_final: 0.7730 (ttt180) REVERT: Q 530 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8137 (ptmt) REVERT: Q 578 GLU cc_start: 0.8945 (pm20) cc_final: 0.8684 (pm20) REVERT: R 566 GLU cc_start: 0.8034 (OUTLIER) cc_final: 0.7752 (pp20) REVERT: S 590 ASN cc_start: 0.8944 (OUTLIER) cc_final: 0.8531 (p0) REVERT: U 486 TYR cc_start: 0.7869 (t80) cc_final: 0.7428 (t80) REVERT: U 566 GLU cc_start: 0.8759 (pp20) cc_final: 0.8374 (pp20) REVERT: U 692 GLU cc_start: 0.8473 (pp20) cc_final: 0.8073 (pp20) REVERT: V 318 LEU cc_start: 0.9171 (OUTLIER) cc_final: 0.8879 (mp) REVERT: V 388 GLN cc_start: 0.8988 (mt0) cc_final: 0.8703 (mm110) REVERT: V 534 GLU cc_start: 0.8598 (mp0) cc_final: 0.8396 (mp0) REVERT: W 350 GLU cc_start: 0.9257 (OUTLIER) cc_final: 0.8929 (mp0) REVERT: W 420 ASP cc_start: 0.8736 (t70) cc_final: 0.8479 (m-30) REVERT: W 720 GLU cc_start: 0.9131 (OUTLIER) cc_final: 0.8637 (mp0) REVERT: X 497 GLN cc_start: 0.8876 (mt0) cc_final: 0.8671 (mt0) REVERT: X 565 GLU cc_start: 0.9112 (mm-30) cc_final: 0.8750 (mm-30) REVERT: X 692 GLU cc_start: 0.8672 (pp20) cc_final: 0.8376 (pp20) REVERT: a 25 MET cc_start: 0.2263 (mmt) cc_final: 0.1963 (mmm) REVERT: a 53 PHE cc_start: 0.4781 (OUTLIER) cc_final: 0.4336 (m-80) REVERT: a 99 TYR cc_start: 0.7947 (t80) cc_final: 0.7651 (t80) REVERT: a 159 TRP cc_start: 0.8651 (p-90) cc_final: 0.8347 (p-90) REVERT: a 173 MET cc_start: 0.7663 (ptm) cc_final: 0.7408 (ptt) REVERT: a 285 TYR cc_start: 0.7680 (OUTLIER) cc_final: 0.7292 (t80) REVERT: b 127 ARG cc_start: 0.8070 (mtt-85) cc_final: 0.7705 (ttm-80) REVERT: b 159 TRP cc_start: 0.6893 (p90) cc_final: 0.6514 (p-90) REVERT: b 173 MET cc_start: 0.8044 (ttm) cc_final: 0.7604 (ttm) REVERT: c 202 ASP cc_start: 0.8180 (t0) cc_final: 0.7787 (t0) REVERT: c 249 GLU cc_start: 0.8898 (mt-10) cc_final: 0.8275 (mp0) REVERT: d 74 MET cc_start: 0.7274 (ttm) cc_final: 0.7011 (ttt) REVERT: d 161 ASN cc_start: 0.7798 (OUTLIER) cc_final: 0.7388 (p0) REVERT: d 181 LYS cc_start: 0.8564 (pttt) cc_final: 0.7880 (pmtt) REVERT: d 245 MET cc_start: 0.8322 (mtp) cc_final: 0.7864 (mtm) REVERT: d 271 ARG cc_start: 0.8078 (tpt-90) cc_final: 0.7799 (tpt170) REVERT: e 153 PHE cc_start: 0.8514 (m-10) cc_final: 0.8306 (m-10) REVERT: e 173 MET cc_start: 0.8495 (mpt) cc_final: 0.7783 (mpt) outliers start: 38 outliers final: 21 residues processed: 457 average time/residue: 0.7470 time to fit residues: 407.4674 Evaluate side-chains 433 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 401 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 586 LEU Chi-restraints excluded: chain E residue 590 ASN Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain I residue 595 ILE Chi-restraints excluded: chain Q residue 454 THR Chi-restraints excluded: chain Q residue 460 THR Chi-restraints excluded: chain Q residue 487 ARG Chi-restraints excluded: chain Q residue 530 LYS Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 549 ASN Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain S residue 590 ASN Chi-restraints excluded: chain U residue 571 THR Chi-restraints excluded: chain V residue 318 LEU Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 350 GLU Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 720 GLU Chi-restraints excluded: chain X residue 460 THR Chi-restraints excluded: chain a residue 53 PHE Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain a residue 285 TYR Chi-restraints excluded: chain b residue 154 TYR Chi-restraints excluded: chain b residue 156 CYS Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 161 ASN Chi-restraints excluded: chain d residue 280 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 432 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 0.0060 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 9.9990 chunk 424 optimal weight: 8.9990 overall best weight: 1.2602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 HIS ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 ASN Q 601 GLN U 488 GLN V 230 HIS V 291 HIS V 337 ASN W 291 HIS a 110 GLN a 210 GLN b 237 HIS b 282 HIS c 237 HIS d 161 ASN e 203 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.120674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.069111 restraints weight = 57350.637| |-----------------------------------------------------------------------------| r_work (start): 0.2851 rms_B_bonded: 2.30 r_work: 0.2733 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2624 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37898 Z= 0.185 Angle : 0.607 8.463 51509 Z= 0.303 Chirality : 0.044 0.188 5437 Planarity : 0.004 0.037 6683 Dihedral : 8.605 134.546 5097 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.06 % Favored : 97.89 % Rotamer: Outliers : 2.35 % Allowed : 12.50 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.12), residues: 4413 helix: 0.69 (0.20), residues: 681 sheet: 0.02 (0.17), residues: 723 loop : -0.36 (0.11), residues: 3009 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG b 253 TYR 0.015 0.002 TYR R 511 PHE 0.024 0.001 PHE e 269 TRP 0.021 0.001 TRP a 272 HIS 0.007 0.001 HIS b 149 Details of bonding type rmsd covalent geometry : bond 0.00434 (37898) covalent geometry : angle 0.60718 (51509) hydrogen bonds : bond 0.03846 ( 785) hydrogen bonds : angle 5.36232 ( 1884) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 515 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 421 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8664 (pp20) cc_final: 0.8336 (pp20) REVERT: F 330 GLU cc_start: 0.8176 (pm20) cc_final: 0.7962 (pm20) REVERT: F 405 MET cc_start: 0.9478 (mtp) cc_final: 0.9195 (mtt) REVERT: F 419 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8538 (pt0) REVERT: F 711 THR cc_start: 0.6872 (OUTLIER) cc_final: 0.5971 (t) REVERT: G 325 GLU cc_start: 0.9096 (OUTLIER) cc_final: 0.8692 (mt-10) REVERT: G 388 GLN cc_start: 0.8753 (mt0) cc_final: 0.8411 (mt0) REVERT: H 577 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8075 (mm-30) REVERT: Q 301 ARG cc_start: 0.9056 (ttm110) cc_final: 0.7505 (mpt180) REVERT: Q 578 GLU cc_start: 0.8893 (pm20) cc_final: 0.8640 (pm20) REVERT: Q 727 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7257 (ppp80) REVERT: R 332 THR cc_start: 0.9159 (m) cc_final: 0.8776 (t) REVERT: R 566 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: S 584 ASP cc_start: 0.9006 (OUTLIER) cc_final: 0.8583 (t70) REVERT: S 590 ASN cc_start: 0.9078 (OUTLIER) cc_final: 0.8651 (p0) REVERT: U 486 TYR cc_start: 0.8002 (t80) cc_final: 0.7463 (t80) REVERT: U 566 GLU cc_start: 0.8780 (pp20) cc_final: 0.8241 (pp20) REVERT: U 692 GLU cc_start: 0.8596 (pp20) cc_final: 0.8075 (pp20) REVERT: V 388 GLN cc_start: 0.8921 (mt0) cc_final: 0.8518 (mm110) REVERT: V 534 GLU cc_start: 0.8668 (mp0) cc_final: 0.8376 (mp0) REVERT: W 420 ASP cc_start: 0.8802 (OUTLIER) cc_final: 0.8537 (m-30) REVERT: W 690 GLN cc_start: 0.8845 (tt0) cc_final: 0.8483 (tt0) REVERT: X 565 GLU cc_start: 0.8884 (mm-30) cc_final: 0.8526 (mm-30) REVERT: a 53 PHE cc_start: 0.4963 (OUTLIER) cc_final: 0.4678 (m-80) REVERT: a 99 TYR cc_start: 0.7846 (t80) cc_final: 0.7476 (t80) REVERT: a 159 TRP cc_start: 0.8743 (p-90) cc_final: 0.8449 (p-90) REVERT: a 173 MET cc_start: 0.8085 (ptm) cc_final: 0.7766 (ptt) REVERT: a 210 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.6868 (tm-30) REVERT: a 285 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7349 (t80) REVERT: b 107 TYR cc_start: 0.7552 (m-80) cc_final: 0.7345 (m-80) REVERT: b 159 TRP cc_start: 0.7012 (p90) cc_final: 0.6601 (p-90) REVERT: b 176 TRP cc_start: 0.8365 (t60) cc_final: 0.8034 (t60) REVERT: b 249 GLU cc_start: 0.8409 (mp0) cc_final: 0.7991 (mp0) REVERT: b 271 ARG cc_start: 0.8494 (tpp80) cc_final: 0.8091 (tpp80) REVERT: c 200 ARG cc_start: 0.8681 (ttm-80) cc_final: 0.8333 (ttm-80) REVERT: c 202 ASP cc_start: 0.8000 (t0) cc_final: 0.7636 (t0) REVERT: c 249 GLU cc_start: 0.9087 (mt-10) cc_final: 0.8299 (mp0) REVERT: d 25 MET cc_start: 0.5547 (mpp) cc_final: 0.5243 (mpt) REVERT: d 74 MET cc_start: 0.7437 (OUTLIER) cc_final: 0.7232 (ttt) REVERT: d 84 LEU cc_start: 0.6732 (tp) cc_final: 0.6526 (tp) REVERT: d 181 LYS cc_start: 0.8470 (pttt) cc_final: 0.8145 (ptpp) REVERT: d 271 ARG cc_start: 0.7995 (tpt-90) cc_final: 0.7681 (tpt170) REVERT: e 153 PHE cc_start: 0.8488 (m-10) cc_final: 0.8262 (m-10) REVERT: e 173 MET cc_start: 0.8460 (mpt) cc_final: 0.8194 (mtm) REVERT: e 224 MET cc_start: 0.9160 (tpp) cc_final: 0.8885 (mmt) REVERT: e 270 PHE cc_start: 0.7924 (m-80) cc_final: 0.7601 (m-80) outliers start: 94 outliers final: 31 residues processed: 485 average time/residue: 0.7018 time to fit residues: 409.2394 Evaluate side-chains 444 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 401 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 711 THR Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 711 THR Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain H residue 692 GLU Chi-restraints excluded: chain I residue 604 LEU Chi-restraints excluded: chain Q residue 727 ARG Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 711 THR Chi-restraints excluded: chain S residue 584 ASP Chi-restraints excluded: chain S residue 590 ASN Chi-restraints excluded: chain V residue 334 THR Chi-restraints excluded: chain V residue 408 THR Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 325 GLU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 382 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain a residue 53 PHE Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 210 GLN Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain a residue 285 TYR Chi-restraints excluded: chain b residue 168 ASP Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 74 MET Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 255 ASP Chi-restraints excluded: chain e residue 261 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 335 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 380 optimal weight: 3.9990 chunk 120 optimal weight: 0.8980 chunk 370 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 20 optimal weight: 0.0980 chunk 274 optimal weight: 0.0570 chunk 292 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 389 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 HIS G 328 GLN G 329 ASN ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 549 ASN U 488 GLN V 230 HIS V 291 HIS V 337 ASN W 291 HIS X 306 ASN b 282 HIS d 161 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.121837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.070568 restraints weight = 56963.213| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 2.29 r_work: 0.2757 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37898 Z= 0.114 Angle : 0.560 9.557 51509 Z= 0.276 Chirality : 0.042 0.192 5437 Planarity : 0.003 0.038 6683 Dihedral : 7.939 134.176 5060 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.95 % Favored : 98.01 % Rotamer: Outliers : 2.40 % Allowed : 12.90 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.12), residues: 4413 helix: 0.74 (0.20), residues: 685 sheet: 0.25 (0.18), residues: 717 loop : -0.28 (0.11), residues: 3011 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG b 253 TYR 0.025 0.001 TYR e 99 PHE 0.011 0.001 PHE d 248 TRP 0.047 0.001 TRP a 272 HIS 0.004 0.001 HIS R 230 Details of bonding type rmsd covalent geometry : bond 0.00259 (37898) covalent geometry : angle 0.56028 (51509) hydrogen bonds : bond 0.03154 ( 785) hydrogen bonds : angle 5.03378 ( 1884) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 422 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8629 (pp20) cc_final: 0.8292 (pp20) REVERT: F 419 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8537 (pt0) REVERT: F 534 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8402 (mp0) REVERT: F 711 THR cc_start: 0.6832 (OUTLIER) cc_final: 0.6632 (t) REVERT: G 556 ASP cc_start: 0.8650 (t70) cc_final: 0.8156 (t0) REVERT: H 567 GLU cc_start: 0.8703 (mp0) cc_final: 0.8029 (mp0) REVERT: H 577 GLU cc_start: 0.8542 (mt-10) cc_final: 0.8094 (mm-30) REVERT: Q 301 ARG cc_start: 0.8996 (ttm110) cc_final: 0.7405 (mpt180) REVERT: Q 578 GLU cc_start: 0.8900 (pm20) cc_final: 0.8640 (pm20) REVERT: Q 727 ARG cc_start: 0.7878 (OUTLIER) cc_final: 0.7095 (ppp80) REVERT: R 326 VAL cc_start: 0.9362 (OUTLIER) cc_final: 0.9113 (t) REVERT: R 332 THR cc_start: 0.9141 (m) cc_final: 0.8773 (t) REVERT: R 350 GLU cc_start: 0.8973 (mp0) cc_final: 0.8725 (mm-30) REVERT: R 566 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: S 584 ASP cc_start: 0.9004 (t0) cc_final: 0.8595 (t70) REVERT: S 590 ASN cc_start: 0.9097 (m110) cc_final: 0.8692 (p0) REVERT: U 486 TYR cc_start: 0.7992 (t80) cc_final: 0.7465 (t80) REVERT: U 566 GLU cc_start: 0.8760 (pp20) cc_final: 0.8482 (pp20) REVERT: U 584 ASP cc_start: 0.8818 (OUTLIER) cc_final: 0.8608 (m-30) REVERT: U 692 GLU cc_start: 0.8588 (pp20) cc_final: 0.8081 (pp20) REVERT: V 388 GLN cc_start: 0.8937 (mt0) cc_final: 0.8529 (mm110) REVERT: V 526 MET cc_start: 0.9475 (mtm) cc_final: 0.9258 (mtp) REVERT: V 533 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8264 (mt-10) REVERT: V 534 GLU cc_start: 0.8693 (mp0) cc_final: 0.8409 (mp0) REVERT: W 420 ASP cc_start: 0.8788 (OUTLIER) cc_final: 0.8546 (m-30) REVERT: W 690 GLN cc_start: 0.8814 (tt0) cc_final: 0.8425 (tt0) REVERT: W 720 GLU cc_start: 0.9260 (OUTLIER) cc_final: 0.8789 (mp0) REVERT: X 565 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8526 (mm-30) REVERT: a 99 TYR cc_start: 0.8032 (t80) cc_final: 0.7737 (t80) REVERT: a 159 TRP cc_start: 0.8731 (p-90) cc_final: 0.8503 (p-90) REVERT: a 173 MET cc_start: 0.8043 (ptm) cc_final: 0.7770 (ptt) REVERT: a 285 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7412 (t80) REVERT: b 127 ARG cc_start: 0.7952 (OUTLIER) cc_final: 0.7519 (ttm-80) REVERT: b 159 TRP cc_start: 0.7098 (p90) cc_final: 0.6618 (p-90) REVERT: b 176 TRP cc_start: 0.8394 (t60) cc_final: 0.8093 (t60) REVERT: b 249 GLU cc_start: 0.8342 (mp0) cc_final: 0.7925 (mp0) REVERT: b 271 ARG cc_start: 0.8528 (tpp80) cc_final: 0.8117 (tpp80) REVERT: c 200 ARG cc_start: 0.8690 (ttm-80) cc_final: 0.8354 (ttm-80) REVERT: c 202 ASP cc_start: 0.7974 (t0) cc_final: 0.7595 (t0) REVERT: c 249 GLU cc_start: 0.9080 (mt-10) cc_final: 0.8291 (mp0) REVERT: d 84 LEU cc_start: 0.6861 (tp) cc_final: 0.6637 (tp) REVERT: d 149 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7053 (m90) REVERT: d 181 LYS cc_start: 0.8379 (pttt) cc_final: 0.7975 (pttp) REVERT: d 271 ARG cc_start: 0.8015 (tpt-90) cc_final: 0.7681 (tpt170) REVERT: d 288 LYS cc_start: 0.7717 (pmtt) cc_final: 0.7449 (pptt) REVERT: e 74 MET cc_start: 0.5135 (mtt) cc_final: 0.3747 (ppp) REVERT: e 153 PHE cc_start: 0.8453 (m-10) cc_final: 0.7988 (m-80) REVERT: e 173 MET cc_start: 0.8473 (mpt) cc_final: 0.8062 (mtm) REVERT: e 224 MET cc_start: 0.9145 (tpp) cc_final: 0.8907 (mmt) REVERT: e 272 TRP cc_start: 0.8521 (t-100) cc_final: 0.8240 (t60) outliers start: 96 outliers final: 42 residues processed: 486 average time/residue: 0.7360 time to fit residues: 428.0863 Evaluate side-chains 461 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 406 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain F residue 325 GLU Chi-restraints excluded: chain F residue 332 THR Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain F residue 711 THR Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain H residue 692 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 586 LEU Chi-restraints excluded: chain I residue 604 LEU Chi-restraints excluded: chain Q residue 727 ARG Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 711 THR Chi-restraints excluded: chain U residue 584 ASP Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain V residue 327 THR Chi-restraints excluded: chain V residue 334 THR Chi-restraints excluded: chain V residue 382 THR Chi-restraints excluded: chain V residue 533 GLU Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 382 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 720 GLU Chi-restraints excluded: chain a residue 25 MET Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 245 MET Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain a residue 285 TYR Chi-restraints excluded: chain b residue 127 ARG Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 132 LEU Chi-restraints excluded: chain d residue 149 HIS Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain e residue 255 ASP Chi-restraints excluded: chain e residue 261 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 440 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 218 optimal weight: 0.7980 chunk 339 optimal weight: 7.9990 chunk 381 optimal weight: 0.9980 chunk 217 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 164 optimal weight: 1.9990 chunk 243 optimal weight: 0.9990 chunk 211 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 HIS F 388 GLN ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 549 ASN V 291 HIS V 337 ASN W 322 GLN ** W 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 110 GLN b 282 HIS d 44 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.120156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.068790 restraints weight = 56920.424| |-----------------------------------------------------------------------------| r_work (start): 0.2841 rms_B_bonded: 2.28 r_work: 0.2720 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.1463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 37898 Z= 0.170 Angle : 0.583 9.543 51509 Z= 0.288 Chirality : 0.043 0.199 5437 Planarity : 0.003 0.035 6683 Dihedral : 7.873 139.366 5056 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.18 % Favored : 97.78 % Rotamer: Outliers : 2.61 % Allowed : 13.35 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.12), residues: 4413 helix: 0.69 (0.20), residues: 687 sheet: 0.28 (0.18), residues: 724 loop : -0.31 (0.11), residues: 3002 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG U 450 TYR 0.022 0.002 TYR b 154 PHE 0.019 0.001 PHE e 270 TRP 0.025 0.001 TRP a 272 HIS 0.006 0.001 HIS b 149 Details of bonding type rmsd covalent geometry : bond 0.00400 (37898) covalent geometry : angle 0.58289 (51509) hydrogen bonds : bond 0.03180 ( 785) hydrogen bonds : angle 4.85011 ( 1884) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 428 time to evaluate : 1.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8664 (pp20) cc_final: 0.8352 (pp20) REVERT: F 236 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8482 (mm) REVERT: F 405 MET cc_start: 0.9497 (mtp) cc_final: 0.9198 (mtt) REVERT: F 419 GLU cc_start: 0.8924 (OUTLIER) cc_final: 0.8568 (pt0) REVERT: F 534 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: G 325 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8704 (mt-10) REVERT: G 556 ASP cc_start: 0.8655 (t70) cc_final: 0.8160 (t0) REVERT: H 567 GLU cc_start: 0.8786 (mp0) cc_final: 0.8124 (mp0) REVERT: H 577 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8111 (mm-30) REVERT: Q 301 ARG cc_start: 0.9041 (ttm110) cc_final: 0.7448 (mpt180) REVERT: Q 578 GLU cc_start: 0.9000 (pm20) cc_final: 0.8627 (pm20) REVERT: Q 727 ARG cc_start: 0.7876 (OUTLIER) cc_final: 0.7216 (ppp80) REVERT: R 329 ASN cc_start: 0.8720 (t0) cc_final: 0.8503 (t160) REVERT: R 332 THR cc_start: 0.9161 (m) cc_final: 0.8792 (t) REVERT: R 350 GLU cc_start: 0.8981 (mp0) cc_final: 0.8717 (mm-30) REVERT: R 526 MET cc_start: 0.9449 (mtm) cc_final: 0.9164 (mtp) REVERT: R 566 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7580 (pp20) REVERT: S 584 ASP cc_start: 0.9027 (OUTLIER) cc_final: 0.8641 (t70) REVERT: S 590 ASN cc_start: 0.9164 (m110) cc_final: 0.8795 (p0) REVERT: U 486 TYR cc_start: 0.8061 (t80) cc_final: 0.7535 (t80) REVERT: U 692 GLU cc_start: 0.8630 (pp20) cc_final: 0.8051 (pp20) REVERT: V 388 GLN cc_start: 0.8956 (mt0) cc_final: 0.8552 (mm110) REVERT: V 533 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.8322 (mt-10) REVERT: V 534 GLU cc_start: 0.8687 (mp0) cc_final: 0.8407 (mp0) REVERT: W 350 GLU cc_start: 0.9375 (OUTLIER) cc_final: 0.8977 (mp0) REVERT: W 420 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8523 (m-30) REVERT: W 690 GLN cc_start: 0.8836 (tt0) cc_final: 0.8488 (tt0) REVERT: X 450 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8365 (ttp-170) REVERT: Y 585 ASN cc_start: 0.8691 (p0) cc_final: 0.8485 (p0) REVERT: Y 588 GLN cc_start: 0.6362 (mm-40) cc_final: 0.5846 (tm130) REVERT: a 97 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7671 (tpp80) REVERT: a 173 MET cc_start: 0.8024 (ptm) cc_final: 0.7770 (ptt) REVERT: a 285 TYR cc_start: 0.7899 (OUTLIER) cc_final: 0.7333 (t80) REVERT: b 107 TYR cc_start: 0.7429 (m-80) cc_final: 0.7217 (m-80) REVERT: b 117 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8154 (tp) REVERT: b 173 MET cc_start: 0.8486 (ttt) cc_final: 0.8091 (ttm) REVERT: b 176 TRP cc_start: 0.8461 (t60) cc_final: 0.8128 (t60) REVERT: b 249 GLU cc_start: 0.8445 (mp0) cc_final: 0.7971 (mp0) REVERT: b 271 ARG cc_start: 0.8542 (tpp80) cc_final: 0.8102 (tpp80) REVERT: c 162 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.8027 (mt-10) REVERT: c 200 ARG cc_start: 0.8767 (ttm-80) cc_final: 0.8400 (ttm-80) REVERT: c 202 ASP cc_start: 0.7981 (t0) cc_final: 0.7605 (t0) REVERT: c 249 GLU cc_start: 0.9066 (mt-10) cc_final: 0.8306 (mp0) REVERT: c 271 ARG cc_start: 0.8449 (tpt-90) cc_final: 0.7556 (tpt-90) REVERT: d 25 MET cc_start: 0.5864 (mpp) cc_final: 0.5492 (mpt) REVERT: d 91 GLU cc_start: 0.6253 (OUTLIER) cc_final: 0.5866 (mp0) REVERT: d 181 LYS cc_start: 0.8300 (pttt) cc_final: 0.8030 (pttt) REVERT: d 229 ASP cc_start: 0.8605 (t0) cc_final: 0.8313 (t0) REVERT: d 271 ARG cc_start: 0.8054 (tpt-90) cc_final: 0.7707 (ttt180) REVERT: d 288 LYS cc_start: 0.7916 (pmtt) cc_final: 0.7520 (pptt) REVERT: e 74 MET cc_start: 0.5208 (mtt) cc_final: 0.3836 (ppp) REVERT: e 224 MET cc_start: 0.9154 (tpp) cc_final: 0.8831 (mmt) REVERT: e 270 PHE cc_start: 0.7751 (m-80) cc_final: 0.7400 (m-80) REVERT: e 272 TRP cc_start: 0.8484 (t-100) cc_final: 0.8250 (t60) outliers start: 104 outliers final: 51 residues processed: 502 average time/residue: 0.7016 time to fit residues: 422.6367 Evaluate side-chains 477 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 411 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain E residue 590 ASN Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 586 LEU Chi-restraints excluded: chain I residue 604 LEU Chi-restraints excluded: chain Q residue 461 GLN Chi-restraints excluded: chain Q residue 727 ARG Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 711 THR Chi-restraints excluded: chain S residue 584 ASP Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain V residue 226 SER Chi-restraints excluded: chain V residue 327 THR Chi-restraints excluded: chain V residue 334 THR Chi-restraints excluded: chain V residue 382 THR Chi-restraints excluded: chain V residue 408 THR Chi-restraints excluded: chain V residue 533 GLU Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 232 ASP Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 325 GLU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 350 GLU Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 382 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 692 GLU Chi-restraints excluded: chain X residue 450 ARG Chi-restraints excluded: chain X residue 700 GLU Chi-restraints excluded: chain a residue 25 MET Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain a residue 285 TYR Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 168 ASP Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 162 GLU Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 91 GLU Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 255 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 64 optimal weight: 1.9990 chunk 437 optimal weight: 1.9990 chunk 238 optimal weight: 2.9990 chunk 226 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 130 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 298 optimal weight: 1.9990 chunk 361 optimal weight: 0.7980 chunk 367 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 HIS ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 GLN ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 702 GLN H 471 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 488 GLN V 291 HIS V 337 ASN W 549 ASN ** W 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 601 GLN ** X 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 589 GLN a 158 ASN b 282 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.119990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.068695 restraints weight = 56781.887| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 2.30 r_work: 0.2718 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 37898 Z= 0.163 Angle : 0.578 9.509 51509 Z= 0.285 Chirality : 0.043 0.388 5437 Planarity : 0.003 0.035 6683 Dihedral : 7.771 143.803 5055 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 2.58 % Allowed : 13.85 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.12), residues: 4413 helix: 0.75 (0.20), residues: 691 sheet: 0.33 (0.18), residues: 724 loop : -0.31 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 253 TYR 0.022 0.001 TYR b 154 PHE 0.015 0.001 PHE d 248 TRP 0.026 0.001 TRP d 272 HIS 0.005 0.001 HIS d 276 Details of bonding type rmsd covalent geometry : bond 0.00385 (37898) covalent geometry : angle 0.57847 (51509) hydrogen bonds : bond 0.02977 ( 785) hydrogen bonds : angle 4.72990 ( 1884) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 525 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 422 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8681 (pp20) cc_final: 0.8365 (pp20) REVERT: F 236 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8489 (mm) REVERT: F 419 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8591 (pt0) REVERT: F 534 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8524 (mp0) REVERT: G 556 ASP cc_start: 0.8665 (t70) cc_final: 0.8153 (t0) REVERT: G 566 GLU cc_start: 0.8708 (OUTLIER) cc_final: 0.8297 (pp20) REVERT: H 567 GLU cc_start: 0.8813 (mp0) cc_final: 0.8507 (mp0) REVERT: H 577 GLU cc_start: 0.8489 (mt-10) cc_final: 0.8100 (mm-30) REVERT: Q 301 ARG cc_start: 0.9068 (ttm110) cc_final: 0.7492 (mpt180) REVERT: R 329 ASN cc_start: 0.8718 (t0) cc_final: 0.8509 (t160) REVERT: R 332 THR cc_start: 0.9147 (m) cc_final: 0.8777 (t) REVERT: R 350 GLU cc_start: 0.8972 (mp0) cc_final: 0.8708 (mm-30) REVERT: R 526 MET cc_start: 0.9468 (mtm) cc_final: 0.9120 (mtp) REVERT: R 566 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: S 584 ASP cc_start: 0.9046 (t0) cc_final: 0.8669 (t70) REVERT: S 590 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8847 (p0) REVERT: U 486 TYR cc_start: 0.8105 (t80) cc_final: 0.7540 (t80) REVERT: U 691 LYS cc_start: 0.8659 (ttpt) cc_final: 0.8399 (ttmm) REVERT: U 692 GLU cc_start: 0.8653 (pp20) cc_final: 0.8057 (pp20) REVERT: V 388 GLN cc_start: 0.8983 (mt0) cc_final: 0.8589 (mm110) REVERT: V 533 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8345 (mt-10) REVERT: V 534 GLU cc_start: 0.8700 (mp0) cc_final: 0.8426 (mp0) REVERT: W 350 GLU cc_start: 0.9383 (OUTLIER) cc_final: 0.8989 (mp0) REVERT: W 420 ASP cc_start: 0.8783 (OUTLIER) cc_final: 0.8530 (m-30) REVERT: W 690 GLN cc_start: 0.8844 (tt0) cc_final: 0.8424 (tt0) REVERT: W 720 GLU cc_start: 0.9262 (OUTLIER) cc_final: 0.8787 (mp0) REVERT: Y 588 GLN cc_start: 0.6544 (mm-40) cc_final: 0.6038 (tm130) REVERT: a 24 TYR cc_start: -0.0075 (OUTLIER) cc_final: -0.0400 (t80) REVERT: a 97 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7710 (tpp80) REVERT: a 173 MET cc_start: 0.8038 (ptm) cc_final: 0.7802 (ptt) REVERT: a 271 ARG cc_start: 0.8278 (tpp-160) cc_final: 0.7521 (tpp80) REVERT: b 107 TYR cc_start: 0.7322 (m-80) cc_final: 0.7120 (m-80) REVERT: b 117 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8194 (tp) REVERT: b 173 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8064 (ttm) REVERT: b 176 TRP cc_start: 0.8508 (t60) cc_final: 0.8157 (t60) REVERT: b 249 GLU cc_start: 0.8417 (mp0) cc_final: 0.7969 (mp0) REVERT: c 162 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8143 (mm-30) REVERT: c 200 ARG cc_start: 0.8752 (ttm-80) cc_final: 0.8374 (ttm-80) REVERT: c 202 ASP cc_start: 0.7984 (t0) cc_final: 0.7603 (t0) REVERT: d 25 MET cc_start: 0.5868 (mpp) cc_final: 0.5572 (mpt) REVERT: d 149 HIS cc_start: 0.7362 (OUTLIER) cc_final: 0.7062 (m90) REVERT: d 181 LYS cc_start: 0.8287 (pttt) cc_final: 0.7925 (pttp) REVERT: d 203 GLN cc_start: 0.7469 (OUTLIER) cc_final: 0.7175 (mp10) REVERT: d 271 ARG cc_start: 0.8060 (tpt-90) cc_final: 0.7565 (tpm-80) REVERT: d 288 LYS cc_start: 0.7896 (pmtt) cc_final: 0.7533 (pptt) REVERT: e 74 MET cc_start: 0.5285 (mtt) cc_final: 0.3984 (ppp) REVERT: e 104 LEU cc_start: 0.8047 (OUTLIER) cc_final: 0.7839 (tp) REVERT: e 153 PHE cc_start: 0.8334 (m-80) cc_final: 0.8101 (m-80) REVERT: e 173 MET cc_start: 0.8454 (OUTLIER) cc_final: 0.8124 (mtt) REVERT: e 272 TRP cc_start: 0.8545 (t-100) cc_final: 0.8291 (t60) outliers start: 103 outliers final: 47 residues processed: 493 average time/residue: 0.7160 time to fit residues: 423.1531 Evaluate side-chains 471 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 406 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 566 GLU Chi-restraints excluded: chain G residue 711 THR Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain H residue 692 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 584 ASP Chi-restraints excluded: chain I residue 586 LEU Chi-restraints excluded: chain I residue 604 LEU Chi-restraints excluded: chain Q residue 461 GLN Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 711 THR Chi-restraints excluded: chain S residue 590 ASN Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain V residue 327 THR Chi-restraints excluded: chain V residue 334 THR Chi-restraints excluded: chain V residue 382 THR Chi-restraints excluded: chain V residue 533 GLU Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 325 GLU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 350 GLU Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 382 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 549 ASN Chi-restraints excluded: chain W residue 720 GLU Chi-restraints excluded: chain a residue 24 TYR Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 245 MET Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 168 ASP Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain c residue 162 GLU Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 149 HIS Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 203 GLN Chi-restraints excluded: chain e residue 104 LEU Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 255 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 213 optimal weight: 2.9990 chunk 309 optimal weight: 0.9990 chunk 448 optimal weight: 10.0000 chunk 318 optimal weight: 20.0000 chunk 354 optimal weight: 7.9990 chunk 217 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 196 optimal weight: 0.6980 chunk 212 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 251 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 589 GLN F 291 HIS ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 499 ASN ** Q 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 291 HIS V 337 ASN W 549 ASN ** W 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 601 GLN ** X 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 41 GLN b 282 HIS c 128 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.119588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.067977 restraints weight = 56971.221| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.32 r_work: 0.2708 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2596 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37898 Z= 0.183 Angle : 0.590 9.466 51509 Z= 0.291 Chirality : 0.044 0.264 5437 Planarity : 0.004 0.038 6683 Dihedral : 7.711 146.432 5052 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.13 % Favored : 97.82 % Rotamer: Outliers : 2.66 % Allowed : 14.15 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.12), residues: 4413 helix: 0.71 (0.20), residues: 692 sheet: 0.34 (0.18), residues: 724 loop : -0.32 (0.11), residues: 2997 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG c 253 TYR 0.021 0.001 TYR b 154 PHE 0.011 0.001 PHE d 269 TRP 0.039 0.001 TRP a 272 HIS 0.005 0.001 HIS R 230 Details of bonding type rmsd covalent geometry : bond 0.00434 (37898) covalent geometry : angle 0.58985 (51509) hydrogen bonds : bond 0.03097 ( 785) hydrogen bonds : angle 4.73226 ( 1884) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 416 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8695 (pp20) cc_final: 0.8374 (pp20) REVERT: F 236 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8478 (mm) REVERT: F 405 MET cc_start: 0.9509 (mtp) cc_final: 0.9252 (mtt) REVERT: F 419 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8599 (pt0) REVERT: F 534 GLU cc_start: 0.8838 (OUTLIER) cc_final: 0.8526 (mp0) REVERT: G 556 ASP cc_start: 0.8686 (t70) cc_final: 0.8174 (t0) REVERT: G 566 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8301 (pp20) REVERT: H 577 GLU cc_start: 0.8477 (mt-10) cc_final: 0.8106 (mm-30) REVERT: Q 301 ARG cc_start: 0.9091 (ttm110) cc_final: 0.7500 (mpt180) REVERT: Q 727 ARG cc_start: 0.8050 (OUTLIER) cc_final: 0.7264 (ppp80) REVERT: R 329 ASN cc_start: 0.8723 (t0) cc_final: 0.8515 (t160) REVERT: R 332 THR cc_start: 0.9147 (m) cc_final: 0.8779 (t) REVERT: R 350 GLU cc_start: 0.8986 (mp0) cc_final: 0.8719 (mm-30) REVERT: R 526 MET cc_start: 0.9466 (mtm) cc_final: 0.9110 (mtp) REVERT: R 566 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7414 (pp20) REVERT: S 584 ASP cc_start: 0.9081 (t0) cc_final: 0.8680 (t70) REVERT: S 590 ASN cc_start: 0.9217 (OUTLIER) cc_final: 0.8861 (p0) REVERT: U 486 TYR cc_start: 0.8123 (t80) cc_final: 0.7539 (t80) REVERT: U 691 LYS cc_start: 0.8708 (ttpt) cc_final: 0.8382 (ttmm) REVERT: U 692 GLU cc_start: 0.8672 (pp20) cc_final: 0.8063 (pp20) REVERT: U 696 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8487 (ttt180) REVERT: V 388 GLN cc_start: 0.8993 (mt0) cc_final: 0.8571 (mm110) REVERT: V 533 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8306 (mt-10) REVERT: V 534 GLU cc_start: 0.8700 (mp0) cc_final: 0.8379 (mp0) REVERT: W 350 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.8985 (mp0) REVERT: W 420 ASP cc_start: 0.8774 (OUTLIER) cc_final: 0.8509 (m-30) REVERT: W 720 GLU cc_start: 0.9273 (OUTLIER) cc_final: 0.8796 (mp0) REVERT: Y 588 GLN cc_start: 0.6633 (mm-40) cc_final: 0.6148 (tm130) REVERT: a 24 TYR cc_start: -0.0230 (OUTLIER) cc_final: -0.0435 (t80) REVERT: a 97 ARG cc_start: 0.8178 (tpp80) cc_final: 0.7863 (tpp80) REVERT: a 173 MET cc_start: 0.8085 (ptm) cc_final: 0.7849 (ptt) REVERT: a 256 HIS cc_start: 0.7510 (OUTLIER) cc_final: 0.7160 (p90) REVERT: b 107 TYR cc_start: 0.7337 (m-80) cc_final: 0.6868 (m-80) REVERT: b 117 LEU cc_start: 0.8611 (OUTLIER) cc_final: 0.8230 (tp) REVERT: b 173 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8273 (ttt) REVERT: b 176 TRP cc_start: 0.8520 (t60) cc_final: 0.8190 (t60) REVERT: b 249 GLU cc_start: 0.8439 (mp0) cc_final: 0.7945 (mp0) REVERT: b 272 TRP cc_start: 0.9066 (t60) cc_final: 0.8846 (t60) REVERT: c 162 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8030 (mm-30) REVERT: c 200 ARG cc_start: 0.8763 (ttm-80) cc_final: 0.8371 (ttm-80) REVERT: c 202 ASP cc_start: 0.7990 (t0) cc_final: 0.7612 (t0) REVERT: c 271 ARG cc_start: 0.8424 (tpt-90) cc_final: 0.8004 (mmm-85) REVERT: d 25 MET cc_start: 0.5855 (OUTLIER) cc_final: 0.5554 (mpt) REVERT: d 149 HIS cc_start: 0.7265 (OUTLIER) cc_final: 0.6986 (m90) REVERT: d 181 LYS cc_start: 0.8311 (pttt) cc_final: 0.8088 (pttt) REVERT: d 203 GLN cc_start: 0.7483 (OUTLIER) cc_final: 0.7220 (mp10) REVERT: d 271 ARG cc_start: 0.8098 (tpt-90) cc_final: 0.7623 (tpm-80) REVERT: d 288 LYS cc_start: 0.7920 (pmtt) cc_final: 0.7571 (pptt) REVERT: e 74 MET cc_start: 0.5306 (OUTLIER) cc_final: 0.4154 (ppp) REVERT: e 173 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8000 (mtt) REVERT: e 272 TRP cc_start: 0.8507 (t-100) cc_final: 0.8268 (t60) outliers start: 106 outliers final: 59 residues processed: 487 average time/residue: 0.7204 time to fit residues: 420.7385 Evaluate side-chains 491 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 410 time to evaluate : 1.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain E residue 590 ASN Chi-restraints excluded: chain F residue 236 LEU Chi-restraints excluded: chain F residue 334 THR Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 408 THR Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 549 ASN Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 566 GLU Chi-restraints excluded: chain G residue 711 THR Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain H residue 692 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain I residue 584 ASP Chi-restraints excluded: chain I residue 586 LEU Chi-restraints excluded: chain I residue 604 LEU Chi-restraints excluded: chain Q residue 461 GLN Chi-restraints excluded: chain Q residue 727 ARG Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 711 THR Chi-restraints excluded: chain S residue 590 ASN Chi-restraints excluded: chain U residue 696 ARG Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain V residue 226 SER Chi-restraints excluded: chain V residue 327 THR Chi-restraints excluded: chain V residue 334 THR Chi-restraints excluded: chain V residue 382 THR Chi-restraints excluded: chain V residue 408 THR Chi-restraints excluded: chain V residue 533 GLU Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 325 GLU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 350 GLU Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 382 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 720 GLU Chi-restraints excluded: chain X residue 571 THR Chi-restraints excluded: chain X residue 595 ILE Chi-restraints excluded: chain a residue 24 TYR Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 245 MET Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 168 ASP Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain b residue 227 VAL Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 162 GLU Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 25 MET Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 149 HIS Chi-restraints excluded: chain d residue 202 ASP Chi-restraints excluded: chain d residue 203 GLN Chi-restraints excluded: chain d residue 224 MET Chi-restraints excluded: chain d residue 280 VAL Chi-restraints excluded: chain e residue 74 MET Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 255 ASP Chi-restraints excluded: chain e residue 271 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 378 optimal weight: 7.9990 chunk 149 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 196 optimal weight: 0.4980 chunk 206 optimal weight: 3.9990 chunk 361 optimal weight: 7.9990 chunk 376 optimal weight: 0.0050 chunk 172 optimal weight: 0.8980 chunk 393 optimal weight: 0.1980 chunk 104 optimal weight: 0.5980 chunk 411 optimal weight: 0.8980 overall best weight: 0.4394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 HIS G 230 HIS ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 291 HIS V 337 ASN W 549 ASN ** W 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 601 GLN X 305 ASN ** X 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 282 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.121308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.070353 restraints weight = 56878.264| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.30 r_work: 0.2751 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2639 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 37898 Z= 0.103 Angle : 0.552 9.070 51509 Z= 0.270 Chirality : 0.041 0.261 5437 Planarity : 0.003 0.033 6683 Dihedral : 7.363 145.747 5052 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.97 % Favored : 97.98 % Rotamer: Outliers : 2.05 % Allowed : 14.70 % Favored : 83.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 4413 helix: 0.81 (0.20), residues: 697 sheet: 0.45 (0.18), residues: 722 loop : -0.26 (0.11), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG e 252 TYR 0.024 0.001 TYR b 154 PHE 0.016 0.001 PHE d 248 TRP 0.035 0.001 TRP d 272 HIS 0.005 0.000 HIS R 230 Details of bonding type rmsd covalent geometry : bond 0.00233 (37898) covalent geometry : angle 0.55220 (51509) hydrogen bonds : bond 0.02617 ( 785) hydrogen bonds : angle 4.55511 ( 1884) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 508 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 426 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8672 (pp20) cc_final: 0.8303 (pp20) REVERT: F 405 MET cc_start: 0.9499 (mtp) cc_final: 0.9231 (mtt) REVERT: F 419 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8656 (pt0) REVERT: F 534 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8506 (mp0) REVERT: G 556 ASP cc_start: 0.8650 (t70) cc_final: 0.8171 (t0) REVERT: G 566 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8299 (pp20) REVERT: H 301 ARG cc_start: 0.8861 (ttm110) cc_final: 0.8639 (ttm110) REVERT: H 567 GLU cc_start: 0.8762 (mp0) cc_final: 0.8453 (mp0) REVERT: H 577 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8086 (mm-30) REVERT: I 588 GLN cc_start: 0.8395 (mt0) cc_final: 0.8016 (pt0) REVERT: Q 301 ARG cc_start: 0.9030 (ttm110) cc_final: 0.7420 (mpt180) REVERT: Q 727 ARG cc_start: 0.8066 (OUTLIER) cc_final: 0.7242 (ppp80) REVERT: R 326 VAL cc_start: 0.9373 (OUTLIER) cc_final: 0.9154 (t) REVERT: R 329 ASN cc_start: 0.8706 (t0) cc_final: 0.8497 (t160) REVERT: R 332 THR cc_start: 0.9128 (m) cc_final: 0.8799 (t) REVERT: R 350 GLU cc_start: 0.8963 (mp0) cc_final: 0.8703 (mm-30) REVERT: R 526 MET cc_start: 0.9462 (mtm) cc_final: 0.9127 (mtp) REVERT: R 566 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7403 (pp20) REVERT: S 584 ASP cc_start: 0.9012 (t0) cc_final: 0.8667 (t70) REVERT: S 590 ASN cc_start: 0.9208 (OUTLIER) cc_final: 0.8886 (p0) REVERT: U 691 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8393 (ttmm) REVERT: U 692 GLU cc_start: 0.8639 (pp20) cc_final: 0.8389 (pp20) REVERT: U 696 ARG cc_start: 0.8886 (OUTLIER) cc_final: 0.8291 (ttt180) REVERT: V 318 LEU cc_start: 0.9168 (OUTLIER) cc_final: 0.8889 (mp) REVERT: V 388 GLN cc_start: 0.8953 (mt0) cc_final: 0.8536 (mm110) REVERT: V 533 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: V 534 GLU cc_start: 0.8711 (mp0) cc_final: 0.8439 (mp0) REVERT: W 350 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.9001 (mp0) REVERT: W 420 ASP cc_start: 0.8793 (OUTLIER) cc_final: 0.8548 (m-30) REVERT: W 720 GLU cc_start: 0.9238 (OUTLIER) cc_final: 0.8777 (mp0) REVERT: X 450 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.8439 (ttp-170) REVERT: Y 588 GLN cc_start: 0.6560 (mm-40) cc_final: 0.6169 (tm130) REVERT: a 97 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7696 (tpp80) REVERT: a 107 TYR cc_start: 0.7127 (m-80) cc_final: 0.6687 (m-80) REVERT: a 162 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7672 (pp20) REVERT: a 173 MET cc_start: 0.8081 (ptm) cc_final: 0.7856 (ptt) REVERT: a 182 MET cc_start: 0.9072 (OUTLIER) cc_final: 0.8732 (tpt) REVERT: a 245 MET cc_start: 0.9172 (OUTLIER) cc_final: 0.8869 (ptp) REVERT: a 271 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.7506 (tpp80) REVERT: b 117 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8187 (tp) REVERT: b 173 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8266 (ttt) REVERT: b 176 TRP cc_start: 0.8482 (t60) cc_final: 0.8142 (t60) REVERT: b 249 GLU cc_start: 0.8342 (mp0) cc_final: 0.7857 (mp0) REVERT: c 162 GLU cc_start: 0.8394 (mt-10) cc_final: 0.8144 (mm-30) REVERT: c 200 ARG cc_start: 0.8775 (ttm-80) cc_final: 0.8376 (ttm-80) REVERT: c 202 ASP cc_start: 0.7934 (t0) cc_final: 0.7558 (t0) REVERT: c 271 ARG cc_start: 0.8436 (tpt-90) cc_final: 0.7992 (mmm-85) REVERT: d 25 MET cc_start: 0.5869 (OUTLIER) cc_final: 0.5634 (mpt) REVERT: d 203 GLN cc_start: 0.7374 (OUTLIER) cc_final: 0.7112 (mp10) REVERT: d 225 CYS cc_start: 0.8889 (m) cc_final: 0.8486 (m) REVERT: d 271 ARG cc_start: 0.8067 (tpt-90) cc_final: 0.7625 (tpm-80) REVERT: d 288 LYS cc_start: 0.7914 (pmtt) cc_final: 0.7587 (pptt) REVERT: e 74 MET cc_start: 0.5269 (OUTLIER) cc_final: 0.4219 (ppp) REVERT: e 173 MET cc_start: 0.8308 (mtm) cc_final: 0.8014 (mtt) REVERT: e 272 TRP cc_start: 0.8494 (t-100) cc_final: 0.8255 (t60) outliers start: 82 outliers final: 38 residues processed: 478 average time/residue: 0.7348 time to fit residues: 420.3000 Evaluate side-chains 473 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 414 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain E residue 590 ASN Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 566 GLU Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain H residue 692 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain Q residue 461 GLN Chi-restraints excluded: chain Q residue 727 ARG Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 711 THR Chi-restraints excluded: chain S residue 590 ASN Chi-restraints excluded: chain U residue 696 ARG Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain V residue 318 LEU Chi-restraints excluded: chain V residue 327 THR Chi-restraints excluded: chain V residue 382 THR Chi-restraints excluded: chain V residue 533 GLU Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 350 GLU Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 549 ASN Chi-restraints excluded: chain W residue 692 GLU Chi-restraints excluded: chain W residue 720 GLU Chi-restraints excluded: chain X residue 450 ARG Chi-restraints excluded: chain X residue 571 THR Chi-restraints excluded: chain a residue 74 MET Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 245 MET Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 25 MET Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 203 GLN Chi-restraints excluded: chain e residue 74 MET Chi-restraints excluded: chain e residue 255 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 408 optimal weight: 0.1980 chunk 321 optimal weight: 10.0000 chunk 385 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 chunk 279 optimal weight: 0.5980 chunk 298 optimal weight: 0.2980 chunk 381 optimal weight: 0.9980 chunk 345 optimal weight: 40.0000 chunk 325 optimal weight: 6.9990 chunk 414 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 HIS F 388 GLN ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 230 HIS ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 337 ASN W 329 ASN W 352 GLN W 549 ASN ** W 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 601 GLN ** X 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 282 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.120392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.069082 restraints weight = 56721.307| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 2.32 r_work: 0.2726 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2615 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 37898 Z= 0.154 Angle : 0.573 9.362 51509 Z= 0.281 Chirality : 0.043 0.316 5437 Planarity : 0.003 0.035 6683 Dihedral : 7.393 146.209 5052 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.04 % Favored : 97.92 % Rotamer: Outliers : 2.00 % Allowed : 14.83 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.12), residues: 4413 helix: 0.82 (0.20), residues: 695 sheet: 0.47 (0.18), residues: 726 loop : -0.28 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG b 97 TYR 0.022 0.001 TYR b 154 PHE 0.010 0.001 PHE d 248 TRP 0.031 0.001 TRP d 272 HIS 0.005 0.001 HIS W 230 Details of bonding type rmsd covalent geometry : bond 0.00364 (37898) covalent geometry : angle 0.57329 (51509) hydrogen bonds : bond 0.02844 ( 785) hydrogen bonds : angle 4.62150 ( 1884) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 501 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 421 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8679 (pp20) cc_final: 0.8358 (pp20) REVERT: F 405 MET cc_start: 0.9524 (mtp) cc_final: 0.9283 (mtt) REVERT: F 419 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8642 (pt0) REVERT: F 534 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8500 (mp0) REVERT: G 556 ASP cc_start: 0.8662 (t70) cc_final: 0.8144 (t0) REVERT: G 566 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8279 (pp20) REVERT: H 577 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8083 (mm-30) REVERT: I 588 GLN cc_start: 0.8425 (mt0) cc_final: 0.8088 (pt0) REVERT: Q 301 ARG cc_start: 0.9081 (ttm110) cc_final: 0.7492 (mpt180) REVERT: Q 727 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7251 (ppp80) REVERT: R 329 ASN cc_start: 0.8706 (t0) cc_final: 0.8492 (t160) REVERT: R 332 THR cc_start: 0.9139 (m) cc_final: 0.8795 (t) REVERT: R 350 GLU cc_start: 0.8977 (mp0) cc_final: 0.8714 (mm-30) REVERT: R 526 MET cc_start: 0.9479 (mtm) cc_final: 0.9141 (mtp) REVERT: R 566 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7405 (pp20) REVERT: S 584 ASP cc_start: 0.9024 (t0) cc_final: 0.8675 (t70) REVERT: S 590 ASN cc_start: 0.9232 (OUTLIER) cc_final: 0.8941 (p0) REVERT: U 691 LYS cc_start: 0.8691 (ttpt) cc_final: 0.8379 (ttmm) REVERT: U 696 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8411 (ttt180) REVERT: V 318 LEU cc_start: 0.9210 (OUTLIER) cc_final: 0.8914 (mp) REVERT: V 388 GLN cc_start: 0.8958 (mt0) cc_final: 0.8511 (mm110) REVERT: V 533 GLU cc_start: 0.8491 (OUTLIER) cc_final: 0.8283 (mt-10) REVERT: V 534 GLU cc_start: 0.8706 (mp0) cc_final: 0.8436 (mp0) REVERT: W 350 GLU cc_start: 0.9378 (OUTLIER) cc_final: 0.8982 (mp0) REVERT: W 420 ASP cc_start: 0.8764 (OUTLIER) cc_final: 0.8516 (m-30) REVERT: Y 588 GLN cc_start: 0.6610 (mm-40) cc_final: 0.6213 (tm130) REVERT: a 24 TYR cc_start: -0.0493 (OUTLIER) cc_final: -0.0902 (t80) REVERT: a 97 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7858 (tpp80) REVERT: a 107 TYR cc_start: 0.7142 (m-80) cc_final: 0.6719 (m-80) REVERT: a 173 MET cc_start: 0.8069 (ptm) cc_final: 0.7828 (ptt) REVERT: a 182 MET cc_start: 0.9073 (OUTLIER) cc_final: 0.8725 (tpt) REVERT: a 244 ARG cc_start: 0.6335 (mtt180) cc_final: 0.6068 (mtt180) REVERT: a 245 MET cc_start: 0.9161 (OUTLIER) cc_final: 0.8828 (ptp) REVERT: a 256 HIS cc_start: 0.7639 (OUTLIER) cc_final: 0.7278 (p90) REVERT: a 271 ARG cc_start: 0.8262 (tpp-160) cc_final: 0.7514 (tpp80) REVERT: b 107 TYR cc_start: 0.7328 (m-80) cc_final: 0.7050 (m-80) REVERT: b 117 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8194 (tp) REVERT: b 173 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8285 (ttt) REVERT: b 176 TRP cc_start: 0.8473 (t60) cc_final: 0.8139 (t60) REVERT: b 249 GLU cc_start: 0.8491 (mp0) cc_final: 0.7965 (mp0) REVERT: b 271 ARG cc_start: 0.8569 (tpp80) cc_final: 0.7954 (tpp80) REVERT: c 162 GLU cc_start: 0.8393 (OUTLIER) cc_final: 0.8144 (mm-30) REVERT: c 200 ARG cc_start: 0.8751 (ttm-80) cc_final: 0.8349 (ttm-80) REVERT: c 202 ASP cc_start: 0.7940 (t0) cc_final: 0.7567 (t0) REVERT: c 271 ARG cc_start: 0.8427 (tpt-90) cc_final: 0.8083 (mmm-85) REVERT: d 25 MET cc_start: 0.5872 (OUTLIER) cc_final: 0.5636 (mpt) REVERT: d 181 LYS cc_start: 0.8186 (pttt) cc_final: 0.7484 (pmtt) REVERT: d 203 GLN cc_start: 0.7414 (OUTLIER) cc_final: 0.7173 (mp10) REVERT: d 271 ARG cc_start: 0.8084 (tpt-90) cc_final: 0.7613 (tpm-80) REVERT: d 288 LYS cc_start: 0.7951 (pmtt) cc_final: 0.7634 (pptt) REVERT: e 74 MET cc_start: 0.5285 (OUTLIER) cc_final: 0.4338 (ppp) REVERT: e 83 TYR cc_start: 0.8126 (m-80) cc_final: 0.7913 (m-80) REVERT: e 173 MET cc_start: 0.8346 (OUTLIER) cc_final: 0.8041 (mtt) REVERT: e 272 TRP cc_start: 0.8509 (t-100) cc_final: 0.8291 (t60) outliers start: 80 outliers final: 46 residues processed: 475 average time/residue: 0.7306 time to fit residues: 414.9836 Evaluate side-chains 476 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 408 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain F residue 549 ASN Chi-restraints excluded: chain F residue 561 MET Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 566 GLU Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain H residue 692 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain Q residue 461 GLN Chi-restraints excluded: chain Q residue 727 ARG Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 711 THR Chi-restraints excluded: chain S residue 590 ASN Chi-restraints excluded: chain U residue 696 ARG Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain V residue 318 LEU Chi-restraints excluded: chain V residue 327 THR Chi-restraints excluded: chain V residue 334 THR Chi-restraints excluded: chain V residue 382 THR Chi-restraints excluded: chain V residue 421 VAL Chi-restraints excluded: chain V residue 533 GLU Chi-restraints excluded: chain V residue 561 MET Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 325 GLU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 350 GLU Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 382 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 549 ASN Chi-restraints excluded: chain W residue 692 GLU Chi-restraints excluded: chain a residue 24 TYR Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 245 MET Chi-restraints excluded: chain a residue 256 HIS Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 162 GLU Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 25 MET Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 203 GLN Chi-restraints excluded: chain e residue 74 MET Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 255 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 83 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 421 optimal weight: 9.9990 chunk 355 optimal weight: 0.0060 chunk 172 optimal weight: 0.7980 chunk 194 optimal weight: 2.9990 chunk 195 optimal weight: 3.9990 chunk 404 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 75 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 291 HIS ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 675 GLN G 230 HIS G 388 GLN ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 471 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 337 ASN ** W 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 601 GLN ** X 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 282 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.121120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.070041 restraints weight = 56846.786| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 2.32 r_work: 0.2747 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2636 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 37898 Z= 0.113 Angle : 0.567 9.343 51509 Z= 0.278 Chirality : 0.042 0.308 5437 Planarity : 0.003 0.036 6683 Dihedral : 7.235 144.104 5052 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 1.99 % Favored : 97.96 % Rotamer: Outliers : 1.83 % Allowed : 15.13 % Favored : 83.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.12), residues: 4413 helix: 0.85 (0.20), residues: 695 sheet: 0.50 (0.18), residues: 728 loop : -0.27 (0.11), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 97 TYR 0.023 0.001 TYR b 154 PHE 0.019 0.001 PHE d 248 TRP 0.041 0.001 TRP d 272 HIS 0.005 0.001 HIS R 230 Details of bonding type rmsd covalent geometry : bond 0.00262 (37898) covalent geometry : angle 0.56699 (51509) hydrogen bonds : bond 0.02704 ( 785) hydrogen bonds : angle 4.56920 ( 1884) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 423 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8670 (pp20) cc_final: 0.8288 (pp20) REVERT: F 405 MET cc_start: 0.9510 (mtp) cc_final: 0.9249 (mtt) REVERT: F 419 GLU cc_start: 0.8919 (OUTLIER) cc_final: 0.8642 (pt0) REVERT: F 534 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8497 (mp0) REVERT: G 556 ASP cc_start: 0.8646 (t70) cc_final: 0.8149 (t0) REVERT: G 566 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8292 (pp20) REVERT: H 577 GLU cc_start: 0.8372 (mt-10) cc_final: 0.8075 (mm-30) REVERT: I 588 GLN cc_start: 0.8416 (mt0) cc_final: 0.8107 (pt0) REVERT: Q 301 ARG cc_start: 0.9048 (ttm110) cc_final: 0.7438 (mpt180) REVERT: Q 727 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7239 (ppp80) REVERT: R 326 VAL cc_start: 0.9375 (OUTLIER) cc_final: 0.9149 (t) REVERT: R 329 ASN cc_start: 0.8707 (t0) cc_final: 0.8503 (t160) REVERT: R 332 THR cc_start: 0.9137 (m) cc_final: 0.8804 (t) REVERT: R 350 GLU cc_start: 0.8970 (mp0) cc_final: 0.8704 (mm-30) REVERT: R 526 MET cc_start: 0.9464 (mtm) cc_final: 0.9125 (mtp) REVERT: R 566 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7392 (pp20) REVERT: S 584 ASP cc_start: 0.9039 (t0) cc_final: 0.8674 (t70) REVERT: S 590 ASN cc_start: 0.9198 (OUTLIER) cc_final: 0.8947 (p0) REVERT: U 691 LYS cc_start: 0.8694 (ttpt) cc_final: 0.8420 (ttmm) REVERT: U 696 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.8273 (ttt180) REVERT: V 318 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8867 (mp) REVERT: V 388 GLN cc_start: 0.8948 (mt0) cc_final: 0.8514 (mm110) REVERT: V 534 GLU cc_start: 0.8714 (mp0) cc_final: 0.8440 (mp0) REVERT: W 350 GLU cc_start: 0.9366 (OUTLIER) cc_final: 0.8972 (mp0) REVERT: W 420 ASP cc_start: 0.8777 (OUTLIER) cc_final: 0.8532 (m-30) REVERT: X 450 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.8346 (ttp-170) REVERT: Y 588 GLN cc_start: 0.6639 (mm-40) cc_final: 0.6282 (tm130) REVERT: a 97 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7763 (tpp80) REVERT: a 107 TYR cc_start: 0.7095 (m-80) cc_final: 0.6623 (m-80) REVERT: a 162 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7675 (pp20) REVERT: a 173 MET cc_start: 0.8054 (ptm) cc_final: 0.7836 (ptt) REVERT: a 182 MET cc_start: 0.9055 (OUTLIER) cc_final: 0.8713 (tpt) REVERT: a 245 MET cc_start: 0.9168 (OUTLIER) cc_final: 0.8893 (ptp) REVERT: a 271 ARG cc_start: 0.8264 (tpp-160) cc_final: 0.7510 (tpp80) REVERT: b 97 ARG cc_start: 0.7436 (ttp-110) cc_final: 0.7175 (ttp-110) REVERT: b 107 TYR cc_start: 0.7278 (m-80) cc_final: 0.7015 (m-80) REVERT: b 117 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8186 (tp) REVERT: b 173 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8302 (ttt) REVERT: b 176 TRP cc_start: 0.8462 (t60) cc_final: 0.8163 (t60) REVERT: b 229 ASP cc_start: 0.8290 (p0) cc_final: 0.7984 (p0) REVERT: b 249 GLU cc_start: 0.8472 (mp0) cc_final: 0.7965 (mp0) REVERT: c 162 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8115 (mm-30) REVERT: c 200 ARG cc_start: 0.8792 (ttm-80) cc_final: 0.8403 (ttm-80) REVERT: c 202 ASP cc_start: 0.7904 (t0) cc_final: 0.7547 (t0) REVERT: c 271 ARG cc_start: 0.8431 (tpt-90) cc_final: 0.8085 (mmm-85) REVERT: d 25 MET cc_start: 0.5879 (OUTLIER) cc_final: 0.5638 (mpt) REVERT: d 181 LYS cc_start: 0.8252 (pttt) cc_final: 0.7521 (pmtt) REVERT: d 203 GLN cc_start: 0.7456 (OUTLIER) cc_final: 0.7238 (mp10) REVERT: d 271 ARG cc_start: 0.8098 (tpt-90) cc_final: 0.7615 (tpm-80) REVERT: d 288 LYS cc_start: 0.7984 (pmtt) cc_final: 0.7657 (pptt) REVERT: e 74 MET cc_start: 0.5293 (mtt) cc_final: 0.4429 (ppp) REVERT: e 173 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.8026 (mtt) REVERT: e 272 TRP cc_start: 0.8474 (t-100) cc_final: 0.8230 (t60) outliers start: 73 outliers final: 38 residues processed: 475 average time/residue: 0.7486 time to fit residues: 424.7482 Evaluate side-chains 472 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 414 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain F residue 352 GLN Chi-restraints excluded: chain F residue 419 GLU Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain G residue 325 GLU Chi-restraints excluded: chain G residue 332 THR Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 566 GLU Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain H residue 692 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain Q residue 727 ARG Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain R residue 711 THR Chi-restraints excluded: chain S residue 590 ASN Chi-restraints excluded: chain U residue 696 ARG Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain V residue 318 LEU Chi-restraints excluded: chain V residue 327 THR Chi-restraints excluded: chain V residue 382 THR Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 325 GLU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 350 GLU Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 382 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 692 GLU Chi-restraints excluded: chain X residue 450 ARG Chi-restraints excluded: chain X residue 571 THR Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 245 MET Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 173 MET Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 162 GLU Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 25 MET Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 203 GLN Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 255 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 63 optimal weight: 2.9990 chunk 405 optimal weight: 9.9990 chunk 179 optimal weight: 3.9990 chunk 89 optimal weight: 0.0980 chunk 391 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 431 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 282 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 230 HIS F 291 HIS ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 601 GLN H 471 ASN ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 337 ASN W 549 ASN ** W 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 601 GLN X 306 ASN ** X 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 601 GLN b 282 HIS ** d 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 158 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.118872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.067527 restraints weight = 56936.273| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 2.28 r_work: 0.2696 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2586 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 37898 Z= 0.223 Angle : 0.624 11.916 51509 Z= 0.309 Chirality : 0.045 0.307 5437 Planarity : 0.004 0.040 6683 Dihedral : 7.518 144.144 5052 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.36 % Favored : 97.60 % Rotamer: Outliers : 1.63 % Allowed : 15.51 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.12), residues: 4413 helix: 0.79 (0.20), residues: 694 sheet: 0.45 (0.18), residues: 720 loop : -0.33 (0.11), residues: 2999 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 97 TYR 0.027 0.002 TYR e 154 PHE 0.013 0.001 PHE V 412 TRP 0.037 0.001 TRP d 272 HIS 0.006 0.001 HIS R 230 Details of bonding type rmsd covalent geometry : bond 0.00533 (37898) covalent geometry : angle 0.62372 (51509) hydrogen bonds : bond 0.03153 ( 785) hydrogen bonds : angle 4.73078 ( 1884) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8826 Ramachandran restraints generated. 4413 Oldfield, 0 Emsley, 4413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 421 time to evaluate : 1.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.8691 (pp20) cc_final: 0.8348 (pp20) REVERT: F 405 MET cc_start: 0.9518 (mtp) cc_final: 0.9270 (mtt) REVERT: F 534 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8514 (mp0) REVERT: G 556 ASP cc_start: 0.8694 (t70) cc_final: 0.8169 (t0) REVERT: G 566 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8285 (pp20) REVERT: H 567 GLU cc_start: 0.8749 (mp0) cc_final: 0.8468 (mp0) REVERT: H 577 GLU cc_start: 0.8389 (mt-10) cc_final: 0.8061 (mm-30) REVERT: I 588 GLN cc_start: 0.8423 (mt0) cc_final: 0.8069 (pt0) REVERT: Q 301 ARG cc_start: 0.9094 (ttm110) cc_final: 0.7505 (mpt180) REVERT: Q 727 ARG cc_start: 0.7945 (OUTLIER) cc_final: 0.7675 (pmm150) REVERT: R 329 ASN cc_start: 0.8712 (t0) cc_final: 0.8492 (t160) REVERT: R 332 THR cc_start: 0.9148 (m) cc_final: 0.8778 (t) REVERT: R 350 GLU cc_start: 0.8980 (mp0) cc_final: 0.8709 (mm-30) REVERT: R 526 MET cc_start: 0.9432 (mtm) cc_final: 0.9143 (mtp) REVERT: R 566 GLU cc_start: 0.7888 (OUTLIER) cc_final: 0.7438 (pp20) REVERT: S 584 ASP cc_start: 0.9062 (t0) cc_final: 0.8747 (t70) REVERT: S 590 ASN cc_start: 0.9256 (OUTLIER) cc_final: 0.8946 (p0) REVERT: U 691 LYS cc_start: 0.8756 (ttpt) cc_final: 0.8435 (ttmm) REVERT: U 696 ARG cc_start: 0.9065 (OUTLIER) cc_final: 0.8436 (ttt180) REVERT: V 388 GLN cc_start: 0.8982 (mt0) cc_final: 0.8537 (mm110) REVERT: V 534 GLU cc_start: 0.8714 (mp0) cc_final: 0.8382 (mp0) REVERT: W 350 GLU cc_start: 0.9374 (OUTLIER) cc_final: 0.9032 (mp0) REVERT: W 420 ASP cc_start: 0.8770 (OUTLIER) cc_final: 0.8512 (m-30) REVERT: X 450 ARG cc_start: 0.8706 (OUTLIER) cc_final: 0.8409 (ttp-170) REVERT: Y 589 GLN cc_start: 0.7524 (mm110) cc_final: 0.7299 (mm110) REVERT: a 24 TYR cc_start: 0.0225 (OUTLIER) cc_final: -0.0285 (t80) REVERT: a 97 ARG cc_start: 0.8229 (tpp80) cc_final: 0.7974 (tpp80) REVERT: a 107 TYR cc_start: 0.7137 (m-80) cc_final: 0.6773 (m-80) REVERT: a 173 MET cc_start: 0.8108 (ptm) cc_final: 0.7872 (ptt) REVERT: a 182 MET cc_start: 0.9067 (OUTLIER) cc_final: 0.8731 (tpt) REVERT: a 271 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7487 (tpp80) REVERT: b 97 ARG cc_start: 0.7550 (ttp-110) cc_final: 0.7283 (ttp-110) REVERT: b 107 TYR cc_start: 0.7277 (m-80) cc_final: 0.6958 (m-80) REVERT: b 117 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8232 (tp) REVERT: b 176 TRP cc_start: 0.8586 (t60) cc_final: 0.8222 (t60) REVERT: b 249 GLU cc_start: 0.8577 (mp0) cc_final: 0.8058 (mp0) REVERT: c 200 ARG cc_start: 0.8769 (ttm-80) cc_final: 0.8379 (ttm-80) REVERT: c 202 ASP cc_start: 0.7942 (t0) cc_final: 0.7581 (t0) REVERT: d 25 MET cc_start: 0.5859 (OUTLIER) cc_final: 0.5652 (mpt) REVERT: d 181 LYS cc_start: 0.8313 (pttt) cc_final: 0.7644 (pmtt) REVERT: d 203 GLN cc_start: 0.7446 (OUTLIER) cc_final: 0.7186 (mp10) REVERT: d 271 ARG cc_start: 0.8114 (tpt-90) cc_final: 0.7639 (tpm-80) REVERT: e 74 MET cc_start: 0.5383 (OUTLIER) cc_final: 0.4463 (ppp) REVERT: e 83 TYR cc_start: 0.8174 (m-80) cc_final: 0.7928 (m-80) REVERT: e 173 MET cc_start: 0.8403 (OUTLIER) cc_final: 0.8051 (mtt) REVERT: e 272 TRP cc_start: 0.8521 (t-100) cc_final: 0.8290 (t60) outliers start: 65 outliers final: 37 residues processed: 467 average time/residue: 0.7245 time to fit residues: 404.4986 Evaluate side-chains 459 residues out of total 3992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 406 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 571 THR Chi-restraints excluded: chain A residue 584 ASP Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain F residue 534 GLU Chi-restraints excluded: chain G residue 337 ASN Chi-restraints excluded: chain G residue 356 VAL Chi-restraints excluded: chain G residue 382 THR Chi-restraints excluded: chain G residue 420 ASP Chi-restraints excluded: chain G residue 566 GLU Chi-restraints excluded: chain H residue 461 GLN Chi-restraints excluded: chain H residue 692 GLU Chi-restraints excluded: chain I residue 390 VAL Chi-restraints excluded: chain Q residue 727 ARG Chi-restraints excluded: chain R residue 226 SER Chi-restraints excluded: chain R residue 326 VAL Chi-restraints excluded: chain R residue 420 ASP Chi-restraints excluded: chain R residue 566 GLU Chi-restraints excluded: chain R residue 598 VAL Chi-restraints excluded: chain S residue 590 ASN Chi-restraints excluded: chain U residue 696 ARG Chi-restraints excluded: chain U residue 738 LEU Chi-restraints excluded: chain V residue 327 THR Chi-restraints excluded: chain V residue 382 THR Chi-restraints excluded: chain V residue 569 LYS Chi-restraints excluded: chain W residue 236 LEU Chi-restraints excluded: chain W residue 325 GLU Chi-restraints excluded: chain W residue 326 VAL Chi-restraints excluded: chain W residue 350 GLU Chi-restraints excluded: chain W residue 356 VAL Chi-restraints excluded: chain W residue 382 THR Chi-restraints excluded: chain W residue 420 ASP Chi-restraints excluded: chain W residue 549 ASN Chi-restraints excluded: chain W residue 692 GLU Chi-restraints excluded: chain X residue 450 ARG Chi-restraints excluded: chain X residue 571 THR Chi-restraints excluded: chain a residue 24 TYR Chi-restraints excluded: chain a residue 101 ILE Chi-restraints excluded: chain a residue 174 VAL Chi-restraints excluded: chain a residue 182 MET Chi-restraints excluded: chain a residue 284 PHE Chi-restraints excluded: chain b residue 117 LEU Chi-restraints excluded: chain b residue 233 THR Chi-restraints excluded: chain b residue 234 THR Chi-restraints excluded: chain c residue 90 VAL Chi-restraints excluded: chain c residue 233 THR Chi-restraints excluded: chain d residue 25 MET Chi-restraints excluded: chain d residue 99 TYR Chi-restraints excluded: chain d residue 130 ILE Chi-restraints excluded: chain d residue 203 GLN Chi-restraints excluded: chain e residue 74 MET Chi-restraints excluded: chain e residue 173 MET Chi-restraints excluded: chain e residue 207 SER Chi-restraints excluded: chain e residue 255 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 450 random chunks: chunk 108 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 164 optimal weight: 1.9990 chunk 271 optimal weight: 0.7980 chunk 287 optimal weight: 0.6980 chunk 321 optimal weight: 7.9990 chunk 317 optimal weight: 5.9990 chunk 404 optimal weight: 1.9990 chunk 30 optimal weight: 0.4980 chunk 57 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 594 GLN F 291 HIS ** F 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 328 GLN ** G 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 352 GLN R 549 ASN ** U 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 337 ASN W 549 ASN ** W 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 601 GLN ** X 572 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 282 HIS ** d 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.119032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.067805 restraints weight = 56755.590| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.25 r_work: 0.2693 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2583 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 37898 Z= 0.195 Angle : 0.701 59.200 51509 Z= 0.372 Chirality : 0.044 0.381 5437 Planarity : 0.004 0.052 6683 Dihedral : 7.530 144.058 5052 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 2.24 % Favored : 97.71 % Rotamer: Outliers : 1.70 % Allowed : 15.43 % Favored : 82.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.12), residues: 4413 helix: 0.77 (0.20), residues: 695 sheet: 0.43 (0.18), residues: 720 loop : -0.34 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG e 97 TYR 0.019 0.002 TYR b 154 PHE 0.012 0.001 PHE V 412 TRP 0.034 0.001 TRP d 272 HIS 0.007 0.001 HIS b 276 Details of bonding type rmsd covalent geometry : bond 0.00456 (37898) covalent geometry : angle 0.70110 (51509) hydrogen bonds : bond 0.03106 ( 785) hydrogen bonds : angle 4.73584 ( 1884) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 22546.99 seconds wall clock time: 381 minutes 38.57 seconds (22898.57 seconds total)