Starting phenix.real_space_refine on Sun Feb 18 12:20:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/02_2024/7q5b_13831.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/02_2024/7q5b_13831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/02_2024/7q5b_13831.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/02_2024/7q5b_13831.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/02_2024/7q5b_13831.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7q5b_13831/02_2024/7q5b_13831.pdb" } resolution = 3.98 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 264 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 166 5.49 5 S 75 5.16 5 C 13330 2.51 5 N 3864 2.21 5 O 4311 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 77": "NH1" <-> "NH2" Residue "A ARG 90": "NH1" <-> "NH2" Residue "A ARG 141": "NH1" <-> "NH2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 237": "OE1" <-> "OE2" Residue "A ARG 241": "NH1" <-> "NH2" Residue "A ASP 257": "OD1" <-> "OD2" Residue "A ARG 269": "NH1" <-> "NH2" Residue "A TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 299": "NH1" <-> "NH2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 351": "OE1" <-> "OE2" Residue "A ARG 364": "NH1" <-> "NH2" Residue "A TYR 389": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 423": "NH1" <-> "NH2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 436": "NH1" <-> "NH2" Residue "B TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 77": "NH1" <-> "NH2" Residue "B ARG 90": "NH1" <-> "NH2" Residue "B ARG 141": "NH1" <-> "NH2" Residue "B ARG 143": "NH1" <-> "NH2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 185": "NH1" <-> "NH2" Residue "B PHE 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 210": "NH1" <-> "NH2" Residue "B ASP 225": "OD1" <-> "OD2" Residue "B ARG 241": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "B TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 299": "NH1" <-> "NH2" Residue "B PHE 306": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 322": "OD1" <-> "OD2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 374": "OD1" <-> "OD2" Residue "B TYR 383": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 401": "NH1" <-> "NH2" Residue "B ARG 451": "NH1" <-> "NH2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "C ASP 22": "OD1" <-> "OD2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 90": "NH1" <-> "NH2" Residue "C TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 165": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 185": "NH1" <-> "NH2" Residue "C PHE 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 200": "OD1" <-> "OD2" Residue "C PHE 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 241": "NH1" <-> "NH2" Residue "C ARG 269": "NH1" <-> "NH2" Residue "C ARG 272": "NH1" <-> "NH2" Residue "C TYR 293": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 299": "NH1" <-> "NH2" Residue "C TYR 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 324": "OE1" <-> "OE2" Residue "C ARG 364": "NH1" <-> "NH2" Residue "C ARG 365": "NH1" <-> "NH2" Residue "C ASP 374": "OD1" <-> "OD2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 412": "OE1" <-> "OE2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 451": "NH1" <-> "NH2" Residue "C GLU 457": "OE1" <-> "OE2" Residue "C ARG 499": "NH1" <-> "NH2" Residue "C ARG 500": "NH1" <-> "NH2" Residue "C PHE 506": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 77": "NH1" <-> "NH2" Residue "D ARG 90": "NH1" <-> "NH2" Residue "D ARG 185": "NH1" <-> "NH2" Residue "D PHE 218": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 241": "NH1" <-> "NH2" Residue "D TYR 274": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 322": "OD1" <-> "OD2" Residue "X TYR 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 108": "OE1" <-> "OE2" Residue "Y PHE 155": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 74": "OE1" <-> "OE2" Residue "Z GLU 77": "OE1" <-> "OE2" Residue "Z GLU 98": "OE1" <-> "OE2" Residue "Z TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 121": "NH1" <-> "NH2" Residue "Z ARG 135": "NH1" <-> "NH2" Residue "Z ASP 145": "OD1" <-> "OD2" Residue "Z PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 218": "NH1" <-> "NH2" Residue "Z ARG 276": "NH1" <-> "NH2" Residue "Z ASP 282": "OD1" <-> "OD2" Residue "Z ARG 286": "NH1" <-> "NH2" Residue "Z ARG 298": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 21746 Number of models: 1 Model: "" Number of chains: 13 Chain: "R" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1140 Classifications: {'DNA': 56} Link IDs: {'rna3p': 55} Chain: "S" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 634 Classifications: {'DNA': 31} Link IDs: {'rna3p': 30} Chain: "r" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 705 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "s" Number of atoms: 185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 185 Classifications: {'DNA': 9} Link IDs: {'rna3p': 8} Chain: "A" Number of atoms: 3438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3438 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 20, 'TRANS': 397} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 3936 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3936 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 24, 'TRANS': 457} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 3912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 482, 3912 Classifications: {'peptide': 482} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 22, 'TRANS': 459} Chain breaks: 2 Unresolved non-hydrogen bonds: 60 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 47 Chain: "D" Number of atoms: 2681 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2681 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 16, 'TRANS': 317} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "X" Number of atoms: 591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 591 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 4, 'TRANS': 65} Chain: "Y" Number of atoms: 1416 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1416 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "Z" Number of atoms: 2328 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2328 Classifications: {'peptide': 289} Link IDs: {'PTRANS': 9, 'TRANS': 279} Chain breaks: 1 Chain: "t" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Chain: "u" Number of atoms: 390 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 390 Classifications: {'DNA': 19} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 18} Time building chain proxies: 11.69, per 1000 atoms: 0.54 Number of scatterers: 21746 At special positions: 0 Unit cell: (151.58, 166.42, 151.58, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 75 16.00 P 166 15.00 O 4311 8.00 N 3864 7.00 C 13330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 134 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.06 Conformation dependent library (CDL) restraints added in 3.6 seconds 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4368 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 13 sheets defined 43.1% alpha, 7.5% beta 75 base pairs and 127 stacking pairs defined. Time for finding SS restraints: 7.46 Creating SS restraints... Processing helix chain 'A' and resid 29 through 38 removed outlier: 3.881A pdb=" N LEU A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N THR A 36 " --> pdb=" O MET A 32 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN A 37 " --> pdb=" O LYS A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 60 removed outlier: 3.637A pdb=" N TYR A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 83 No H-bonds generated for 'chain 'A' and resid 81 through 83' Processing helix chain 'A' and resid 84 through 92 Processing helix chain 'A' and resid 103 through 112 Processing helix chain 'A' and resid 119 through 129 Processing helix chain 'A' and resid 131 through 138 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 227 through 232 Processing helix chain 'A' and resid 232 through 243 removed outlier: 3.614A pdb=" N LEU A 238 " --> pdb=" O LYS A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 257 removed outlier: 4.057A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 275 Processing helix chain 'A' and resid 281 through 296 removed outlier: 4.350A pdb=" N TYR A 285 " --> pdb=" O ASN A 281 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 304 through 309 Processing helix chain 'A' and resid 334 through 362 removed outlier: 3.753A pdb=" N HIS A 338 " --> pdb=" O GLU A 334 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'B' and resid 29 through 38 removed outlier: 3.771A pdb=" N LEU B 35 " --> pdb=" O HIS B 31 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N THR B 36 " --> pdb=" O MET B 32 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N GLN B 37 " --> pdb=" O LYS B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 60 removed outlier: 4.026A pdb=" N TYR B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 83 No H-bonds generated for 'chain 'B' and resid 81 through 83' Processing helix chain 'B' and resid 84 through 94 Processing helix chain 'B' and resid 95 through 98 removed outlier: 3.739A pdb=" N PHE B 98 " --> pdb=" O HIS B 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 95 through 98' Processing helix chain 'B' and resid 103 through 112 Processing helix chain 'B' and resid 119 through 131 Processing helix chain 'B' and resid 133 through 138 removed outlier: 3.757A pdb=" N LYS B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 145 removed outlier: 3.578A pdb=" N LEU B 144 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 215 Processing helix chain 'B' and resid 232 through 242 Processing helix chain 'B' and resid 253 through 256 removed outlier: 3.545A pdb=" N THR B 256 " --> pdb=" O HIS B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 257 through 275 removed outlier: 3.732A pdb=" N ARG B 269 " --> pdb=" O GLN B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 296 removed outlier: 3.800A pdb=" N GLN B 288 " --> pdb=" O VAL B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 311 removed outlier: 3.912A pdb=" N ASP B 309 " --> pdb=" O PRO B 305 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 328 removed outlier: 3.539A pdb=" N ARG B 328 " --> pdb=" O VAL B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 362 removed outlier: 4.042A pdb=" N HIS B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ASN B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASN B 361 " --> pdb=" O MET B 357 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ASN B 362 " --> pdb=" O GLU B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 454 removed outlier: 3.819A pdb=" N LYS B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG B 454 " --> pdb=" O GLU B 450 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 449 through 454' Processing helix chain 'B' and resid 487 through 491 Processing helix chain 'B' and resid 499 through 504 removed outlier: 3.840A pdb=" N LEU B 503 " --> pdb=" O ARG B 499 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 34 Processing helix chain 'C' and resid 47 through 60 removed outlier: 3.510A pdb=" N TYR C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLN C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 84 through 94 Processing helix chain 'C' and resid 103 through 112 removed outlier: 3.673A pdb=" N SER C 112 " --> pdb=" O LEU C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 119 through 132 Processing helix chain 'C' and resid 204 through 213 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 258 through 275 removed outlier: 3.806A pdb=" N ARG C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 296 Processing helix chain 'C' and resid 304 through 309 removed outlier: 3.825A pdb=" N ASP C 309 " --> pdb=" O PRO C 305 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 340 Processing helix chain 'C' and resid 341 through 352 removed outlier: 3.770A pdb=" N GLN C 345 " --> pdb=" O ALA C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 426 through 428 No H-bonds generated for 'chain 'C' and resid 426 through 428' Processing helix chain 'C' and resid 447 through 454 removed outlier: 3.686A pdb=" N LYS C 453 " --> pdb=" O THR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 511 Processing helix chain 'D' and resid 28 through 34 removed outlier: 4.173A pdb=" N MET D 32 " --> pdb=" O VAL D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 60 removed outlier: 3.557A pdb=" N TYR D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 84 through 94 Processing helix chain 'D' and resid 95 through 98 removed outlier: 3.809A pdb=" N PHE D 98 " --> pdb=" O HIS D 95 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 95 through 98' Processing helix chain 'D' and resid 103 through 112 Processing helix chain 'D' and resid 119 through 131 Processing helix chain 'D' and resid 204 through 214 Processing helix chain 'D' and resid 233 through 242 Processing helix chain 'D' and resid 258 through 275 removed outlier: 4.090A pdb=" N LEU D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ASN D 268 " --> pdb=" O ILE D 264 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ARG D 269 " --> pdb=" O GLN D 265 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU D 270 " --> pdb=" O THR D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 285 through 295 Processing helix chain 'D' and resid 304 through 310 removed outlier: 3.846A pdb=" N ASP D 309 " --> pdb=" O PRO D 305 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 363 removed outlier: 3.577A pdb=" N HIS D 338 " --> pdb=" O GLU D 334 " (cutoff:3.500A) Processing helix chain 'X' and resid 422 through 435 Processing helix chain 'X' and resid 438 through 446 Processing helix chain 'X' and resid 450 through 465 removed outlier: 3.856A pdb=" N LYS X 463 " --> pdb=" O VAL X 459 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS X 464 " --> pdb=" O ASN X 460 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG X 465 " --> pdb=" O GLU X 461 " (cutoff:3.500A) Processing helix chain 'X' and resid 465 through 476 removed outlier: 3.600A pdb=" N GLU X 470 " --> pdb=" O PRO X 466 " (cutoff:3.500A) Processing helix chain 'X' and resid 481 through 489 removed outlier: 4.158A pdb=" N GLU X 487 " --> pdb=" O GLU X 483 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE X 488 " --> pdb=" O TYR X 484 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS X 489 " --> pdb=" O CYS X 485 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 88 Processing helix chain 'Y' and resid 128 through 147 removed outlier: 3.862A pdb=" N GLY Y 147 " --> pdb=" O ILE Y 143 " (cutoff:3.500A) Processing helix chain 'Y' and resid 172 through 179 Processing helix chain 'Y' and resid 220 through 237 Proline residue: Y 232 - end of helix Processing helix chain 'Z' and resid 72 through 95 removed outlier: 3.916A pdb=" N ARG Z 76 " --> pdb=" O ALA Z 72 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLU Z 77 " --> pdb=" O LEU Z 73 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA Z 78 " --> pdb=" O GLU Z 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR Z 79 " --> pdb=" O SER Z 75 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ALA Z 93 " --> pdb=" O ALA Z 89 " (cutoff:3.500A) Processing helix chain 'Z' and resid 97 through 114 Processing helix chain 'Z' and resid 121 through 137 removed outlier: 3.714A pdb=" N VAL Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU Z 137 " --> pdb=" O ALA Z 133 " (cutoff:3.500A) Processing helix chain 'Z' and resid 142 through 147 Processing helix chain 'Z' and resid 153 through 169 removed outlier: 3.738A pdb=" N ILE Z 157 " --> pdb=" O SER Z 153 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LYS Z 166 " --> pdb=" O LEU Z 162 " (cutoff:3.500A) Processing helix chain 'Z' and resid 178 through 186 removed outlier: 3.547A pdb=" N ILE Z 182 " --> pdb=" O PRO Z 178 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N GLN Z 183 " --> pdb=" O SER Z 179 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N HIS Z 184 " --> pdb=" O LEU Z 180 " (cutoff:3.500A) Processing helix chain 'Z' and resid 196 through 211 removed outlier: 3.508A pdb=" N LYS Z 200 " --> pdb=" O ILE Z 196 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG Z 208 " --> pdb=" O LYS Z 204 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS Z 211 " --> pdb=" O GLN Z 207 " (cutoff:3.500A) Processing helix chain 'Z' and resid 219 through 235 Processing helix chain 'Z' and resid 241 through 247 removed outlier: 3.852A pdb=" N ILE Z 244 " --> pdb=" O HIS Z 241 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL Z 245 " --> pdb=" O THR Z 242 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Z 246 " --> pdb=" O GLU Z 243 " (cutoff:3.500A) Processing helix chain 'Z' and resid 251 through 266 Processing helix chain 'Z' and resid 287 through 294 Processing helix chain 'Z' and resid 448 through 455 removed outlier: 4.043A pdb=" N VAL Z 455 " --> pdb=" O TYR Z 451 " (cutoff:3.500A) Processing helix chain 'Z' and resid 476 through 478 No H-bonds generated for 'chain 'Z' and resid 476 through 478' Processing helix chain 'Z' and resid 479 through 491 removed outlier: 3.854A pdb=" N ILE Z 486 " --> pdb=" O LEU Z 482 " (cutoff:3.500A) Processing helix chain 'Z' and resid 492 through 497 removed outlier: 4.062A pdb=" N LEU Z 496 " --> pdb=" O ALA Z 492 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLU Z 497 " --> pdb=" O ASP Z 493 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 492 through 497' Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 193 through 195 removed outlier: 4.169A pdb=" N ASP A 164 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL A 183 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ILE A 161 " --> pdb=" O THR A 223 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 402 through 407 removed outlier: 6.365A pdb=" N LYS A 405 " --> pdb=" O GLU A 412 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N GLU A 412 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASN A 407 " --> pdb=" O ALA A 410 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ALA A 410 " --> pdb=" O ASN A 407 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ILE A 425 " --> pdb=" O TYR A 411 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 66 through 68 Processing sheet with id=AA5, first strand: chain 'B' and resid 162 through 165 removed outlier: 3.534A pdb=" N SER B 162 " --> pdb=" O VAL B 183 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASP B 164 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL B 181 " --> pdb=" O ASP B 164 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LEU B 180 " --> pdb=" O ILE B 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 424 through 426 removed outlier: 3.578A pdb=" N TYR B 411 " --> pdb=" O ILE B 425 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA B 410 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N LYS B 405 " --> pdb=" O ALA B 410 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N GLU B 412 " --> pdb=" O VAL B 403 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 458 through 464 removed outlier: 6.595A pdb=" N HIS B 474 " --> pdb=" O THR B 459 " (cutoff:3.500A) removed outlier: 5.525A pdb=" N LEU B 461 " --> pdb=" O LEU B 472 " (cutoff:3.500A) removed outlier: 8.083A pdb=" N LEU B 472 " --> pdb=" O LEU B 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 192 through 193 Processing sheet with id=AA9, first strand: chain 'C' and resid 424 through 425 removed outlier: 3.629A pdb=" N ILE C 425 " --> pdb=" O TYR C 411 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ALA C 410 " --> pdb=" O ILE C 406 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS C 404 " --> pdb=" O GLU C 412 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU C 377 " --> pdb=" O LYS C 431 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 458 through 464 removed outlier: 6.920A pdb=" N LEU C 472 " --> pdb=" O ILE C 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 66 through 68 removed outlier: 3.706A pdb=" N TYR D 73 " --> pdb=" O SER D 66 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU D 68 " --> pdb=" O MET D 71 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 190 through 195 removed outlier: 4.096A pdb=" N VAL D 181 " --> pdb=" O ASP D 164 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 164 " --> pdb=" O VAL D 181 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE D 161 " --> pdb=" O THR D 221 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Y' and resid 92 through 93 removed outlier: 3.727A pdb=" N GLY Y 125 " --> pdb=" O ILE Y 70 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N ILE Y 70 " --> pdb=" O GLY Y 125 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N LEU Y 67 " --> pdb=" O SER Y 163 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N SER Y 163 " --> pdb=" O LEU Y 67 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR Y 73 " --> pdb=" O ILE Y 157 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ILE Y 157 " --> pdb=" O THR Y 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N GLY Y 162 " --> pdb=" O LEU Y 214 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Y 215 " --> pdb=" O VAL Y 203 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N GLU Y 186 " --> pdb=" O PHE Y 190 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY Y 192 " --> pdb=" O SER Y 184 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N SER Y 184 " --> pdb=" O GLY Y 192 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1845 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 176 hydrogen bonds 352 hydrogen bond angles 0 basepair planarities 75 basepair parallelities 127 stacking parallelities Total time for adding SS restraints: 7.37 Time building geometry restraints manager: 9.69 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: 5073 1.33 - 1.45: 5262 1.45 - 1.57: 11760 1.57 - 1.69: 330 1.69 - 1.81: 126 Bond restraints: 22551 Sorted by residual: bond pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 1.457 1.519 -0.062 1.29e-02 6.01e+03 2.30e+01 bond pdb=" N TYR C 74 " pdb=" CA TYR C 74 " ideal model delta sigma weight residual 1.457 1.515 -0.058 1.29e-02 6.01e+03 2.01e+01 bond pdb=" C GLN C 75 " pdb=" O GLN C 75 " ideal model delta sigma weight residual 1.235 1.291 -0.056 1.26e-02 6.30e+03 1.95e+01 bond pdb=" CA TYR C 74 " pdb=" C TYR C 74 " ideal model delta sigma weight residual 1.523 1.557 -0.034 1.34e-02 5.57e+03 6.32e+00 bond pdb=" C GLN C 75 " pdb=" N ASP C 76 " ideal model delta sigma weight residual 1.333 1.369 -0.036 1.56e-02 4.11e+03 5.42e+00 ... (remaining 22546 not shown) Histogram of bond angle deviations from ideal: 98.61 - 106.45: 1587 106.45 - 114.29: 13024 114.29 - 122.13: 12230 122.13 - 129.97: 4171 129.97 - 137.82: 204 Bond angle restraints: 31216 Sorted by residual: angle pdb=" C GLN C 75 " pdb=" N ASP C 76 " pdb=" CA ASP C 76 " ideal model delta sigma weight residual 122.79 104.00 18.79 1.63e+00 3.76e-01 1.33e+02 angle pdb=" C TYR C 74 " pdb=" N GLN C 75 " pdb=" CA GLN C 75 " ideal model delta sigma weight residual 121.54 137.82 -16.28 1.91e+00 2.74e-01 7.26e+01 angle pdb=" N PRO D 150 " pdb=" CA PRO D 150 " pdb=" CB PRO D 150 " ideal model delta sigma weight residual 103.25 111.59 -8.34 1.05e+00 9.07e-01 6.31e+01 angle pdb=" N PRO D 254 " pdb=" CA PRO D 254 " pdb=" CB PRO D 254 " ideal model delta sigma weight residual 103.25 111.15 -7.90 1.05e+00 9.07e-01 5.66e+01 angle pdb=" N PRO D 152 " pdb=" CA PRO D 152 " pdb=" CB PRO D 152 " ideal model delta sigma weight residual 103.25 111.07 -7.82 1.05e+00 9.07e-01 5.55e+01 ... (remaining 31211 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 12459 35.90 - 71.79: 812 71.79 - 107.69: 23 107.69 - 143.59: 9 143.59 - 179.48: 11 Dihedral angle restraints: 13314 sinusoidal: 6606 harmonic: 6708 Sorted by residual: dihedral pdb=" CA THR A 231 " pdb=" C THR A 231 " pdb=" N ALA A 232 " pdb=" CA ALA A 232 " ideal model delta harmonic sigma weight residual 180.00 141.22 38.78 0 5.00e+00 4.00e-02 6.02e+01 dihedral pdb=" CA LYS B 421 " pdb=" C LYS B 421 " pdb=" N HIS B 422 " pdb=" CA HIS B 422 " ideal model delta harmonic sigma weight residual 180.00 145.85 34.15 0 5.00e+00 4.00e-02 4.67e+01 dihedral pdb=" CA VAL D 292 " pdb=" C VAL D 292 " pdb=" N TYR D 293 " pdb=" CA TYR D 293 " ideal model delta harmonic sigma weight residual 180.00 148.33 31.67 0 5.00e+00 4.00e-02 4.01e+01 ... (remaining 13311 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 3223 0.091 - 0.182: 265 0.182 - 0.272: 24 0.272 - 0.363: 2 0.363 - 0.454: 2 Chirality restraints: 3516 Sorted by residual: chirality pdb=" CB ILE A 395 " pdb=" CA ILE A 395 " pdb=" CG1 ILE A 395 " pdb=" CG2 ILE A 395 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CB ILE B 153 " pdb=" CA ILE B 153 " pdb=" CG1 ILE B 153 " pdb=" CG2 ILE B 153 " both_signs ideal model delta sigma weight residual False 2.64 2.22 0.42 2.00e-01 2.50e+01 4.45e+00 chirality pdb=" CB THR D 41 " pdb=" CA THR D 41 " pdb=" OG1 THR D 41 " pdb=" CG2 THR D 41 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.08e+00 ... (remaining 3513 not shown) Planarity restraints: 3379 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN C 75 " 0.017 2.00e-02 2.50e+03 3.46e-02 1.20e+01 pdb=" C GLN C 75 " -0.060 2.00e-02 2.50e+03 pdb=" O GLN C 75 " 0.021 2.00e-02 2.50e+03 pdb=" N ASP C 76 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 494 " 0.050 5.00e-02 4.00e+02 7.65e-02 9.35e+00 pdb=" N PRO C 495 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 495 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO C 495 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 366 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.84e+00 pdb=" N PRO C 367 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO C 367 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 367 " 0.039 5.00e-02 4.00e+02 ... (remaining 3376 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 3419 2.76 - 3.30: 20381 3.30 - 3.83: 38624 3.83 - 4.37: 43357 4.37 - 4.90: 68937 Nonbonded interactions: 174718 Sorted by model distance: nonbonded pdb=" O CYS Z 134 " pdb=" OG1 THR Z 139 " model vdw 2.231 2.440 nonbonded pdb=" OG1 THR B 202 " pdb=" O ARG B 229 " model vdw 2.234 2.440 nonbonded pdb=" O ILE B 222 " pdb=" OG1 THR B 247 " model vdw 2.238 2.440 nonbonded pdb=" O LEU A 342 " pdb=" OG1 THR A 346 " model vdw 2.266 2.440 nonbonded pdb=" NH1 ARG B 185 " pdb=" OP1 DT u 5 " model vdw 2.274 2.520 ... (remaining 174713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 18 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 142 or (resid 143 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 353 or (resid 356 through 361 \ and (name N or name CA or name C or name O or name CB )) or resid 362 through 38 \ 4 or (resid 389 and (name N or name CA or name C or name O or name CB )) or resi \ d 390 through 395 or (resid 396 and (name N or name CA or name C or name O or na \ me CB )) or resid 397 through 437)) selection = (chain 'B' and ((resid 18 through 20 and (name N or name CA or name C or name O \ or name CB )) or resid 21 through 142 or (resid 143 and (name N or name CA or na \ me C or name O or name CB )) or resid 154 through 197 or resid 201 through 353 o \ r (resid 356 through 361 and (name N or name CA or name C or name O or name CB ) \ ) or resid 362 through 395 or (resid 396 and (name N or name CA or name C or nam \ e O or name CB )) or resid 397 through 437)) selection = (chain 'C' and (resid 18 through 197 or resid 201 through 384 or (resid 389 and \ (name N or name CA or name C or name O or name CB )) or resid 390 through 436 or \ (resid 437 and (name N or name CA or name C or name O or name CB )))) } ncs_group { reference = chain 't' selection = chain 'u' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.020 Extract box with map and model: 6.990 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 61.080 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6056 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 0.077 22551 Z= 0.267 Angle : 0.908 18.793 31216 Z= 0.509 Chirality : 0.053 0.454 3516 Planarity : 0.006 0.076 3379 Dihedral : 21.260 179.482 8943 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.22 % Allowed : 13.23 % Favored : 86.55 % Rotamer: Outliers : 0.10 % Allowed : 0.60 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.17), residues: 2223 helix: -0.76 (0.16), residues: 837 sheet: -1.64 (0.48), residues: 100 loop : -2.84 (0.16), residues: 1286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 117 HIS 0.014 0.001 HIS Z 473 PHE 0.045 0.002 PHE C 306 TYR 0.024 0.002 TYR Z 155 ARG 0.005 0.000 ARG D 269 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 379 time to evaluate : 2.409 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 31 HIS cc_start: 0.5508 (m90) cc_final: 0.5226 (m170) REVERT: A 73 TYR cc_start: 0.5812 (p90) cc_final: 0.5298 (p90) REVERT: B 89 MET cc_start: 0.7192 (ptp) cc_final: 0.6333 (ptp) REVERT: B 283 HIS cc_start: 0.6531 (p-80) cc_final: 0.6265 (p-80) REVERT: B 330 PHE cc_start: 0.5167 (p90) cc_final: 0.4581 (p90) REVERT: C 90 ARG cc_start: 0.6239 (tpt-90) cc_final: 0.5975 (tpp-160) REVERT: C 115 TYR cc_start: 0.6461 (m-10) cc_final: 0.6232 (m-10) REVERT: C 272 ARG cc_start: 0.6261 (ttt180) cc_final: 0.5908 (tpp80) REVERT: D 137 ILE cc_start: 0.7105 (mt) cc_final: 0.6890 (mt) REVERT: D 291 PHE cc_start: 0.7435 (t80) cc_final: 0.7183 (t80) REVERT: Y 97 LYS cc_start: 0.5565 (mttt) cc_final: 0.4885 (pttm) REVERT: Y 114 LEU cc_start: 0.7739 (tp) cc_final: 0.7293 (tp) REVERT: Y 131 ASP cc_start: 0.8210 (m-30) cc_final: 0.7923 (m-30) REVERT: Y 206 ILE cc_start: 0.7042 (mm) cc_final: 0.6780 (mm) REVERT: Y 233 VAL cc_start: 0.7899 (t) cc_final: 0.7542 (t) REVERT: Y 240 MET cc_start: 0.4399 (mtm) cc_final: 0.3320 (tpp) REVERT: Z 130 LEU cc_start: 0.7387 (mt) cc_final: 0.7024 (mt) REVERT: Z 460 ASP cc_start: 0.5980 (m-30) cc_final: 0.5574 (t0) REVERT: Z 494 PHE cc_start: 0.4215 (t80) cc_final: 0.2628 (m-80) outliers start: 2 outliers final: 1 residues processed: 380 average time/residue: 0.3677 time to fit residues: 209.1461 Evaluate side-chains 211 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 210 time to evaluate : 2.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 199 optimal weight: 0.1980 chunk 178 optimal weight: 7.9990 chunk 99 optimal weight: 0.0470 chunk 61 optimal weight: 0.0970 chunk 120 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 184 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 112 optimal weight: 7.9990 chunk 137 optimal weight: 0.0670 chunk 214 optimal weight: 10.0000 overall best weight: 0.2814 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN C 416 ASN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 203 GLN ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 141 HIS Z 207 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6103 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22551 Z= 0.184 Angle : 0.682 12.823 31216 Z= 0.367 Chirality : 0.042 0.203 3516 Planarity : 0.005 0.066 3379 Dihedral : 23.890 179.060 4372 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.06 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.87 % Favored : 87.04 % Rotamer: Outliers : 1.24 % Allowed : 9.55 % Favored : 89.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.17), residues: 2223 helix: -0.11 (0.18), residues: 857 sheet: -1.61 (0.45), residues: 106 loop : -2.76 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP Z 213 HIS 0.008 0.001 HIS D 122 PHE 0.026 0.002 PHE A 213 TYR 0.021 0.001 TYR C 389 ARG 0.010 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 235 time to evaluate : 2.174 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 45 MET cc_start: 0.6872 (mmp) cc_final: 0.5905 (mtp) REVERT: B 283 HIS cc_start: 0.6509 (p-80) cc_final: 0.6280 (p-80) REVERT: B 330 PHE cc_start: 0.5094 (p90) cc_final: 0.4521 (p90) REVERT: C 71 MET cc_start: 0.3888 (mmm) cc_final: 0.3656 (mmt) REVERT: C 90 ARG cc_start: 0.6288 (tpt-90) cc_final: 0.6064 (tpp-160) REVERT: D 128 ILE cc_start: 0.7269 (mm) cc_final: 0.7011 (pt) REVERT: D 215 TYR cc_start: 0.5660 (m-10) cc_final: 0.5298 (m-10) REVERT: Y 97 LYS cc_start: 0.5555 (mttt) cc_final: 0.4861 (pttm) REVERT: Y 131 ASP cc_start: 0.8252 (m-30) cc_final: 0.8017 (m-30) REVERT: Y 240 MET cc_start: 0.4867 (mtm) cc_final: 0.3434 (tpp) REVERT: Z 460 ASP cc_start: 0.6004 (m-30) cc_final: 0.5626 (t0) REVERT: Z 494 PHE cc_start: 0.4365 (t80) cc_final: 0.2811 (m-80) outliers start: 25 outliers final: 15 residues processed: 249 average time/residue: 0.3477 time to fit residues: 133.2385 Evaluate side-chains 213 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 198 time to evaluate : 2.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 122 HIS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 154 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 0.9990 chunk 178 optimal weight: 0.5980 chunk 145 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 214 optimal weight: 7.9990 chunk 231 optimal weight: 8.9990 chunk 191 optimal weight: 5.9990 chunk 212 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 172 optimal weight: 3.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN A 177 ASN A 278 ASN ** B 362 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 505 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 22551 Z= 0.283 Angle : 0.746 11.269 31216 Z= 0.400 Chirality : 0.046 0.231 3516 Planarity : 0.006 0.066 3379 Dihedral : 24.184 178.732 4372 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 20.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.68 % Favored : 86.19 % Rotamer: Outliers : 2.79 % Allowed : 14.18 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.17), residues: 2223 helix: -0.10 (0.18), residues: 856 sheet: -1.71 (0.45), residues: 108 loop : -2.87 (0.17), residues: 1259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.004 TRP Z 213 HIS 0.012 0.002 HIS A 95 PHE 0.032 0.002 PHE C 306 TYR 0.028 0.002 TYR B 435 ARG 0.005 0.001 ARG C 507 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 215 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 MET cc_start: 0.7360 (ptp) cc_final: 0.6427 (ptp) REVERT: B 230 MET cc_start: 0.8021 (OUTLIER) cc_final: 0.7813 (mtm) REVERT: B 283 HIS cc_start: 0.6854 (p-80) cc_final: 0.6535 (p-80) REVERT: B 328 ARG cc_start: 0.5802 (tpt-90) cc_final: 0.4857 (tpt90) REVERT: B 390 MET cc_start: 0.6110 (ptt) cc_final: 0.5701 (mtt) REVERT: C 71 MET cc_start: 0.4028 (mmm) cc_final: 0.3573 (mmt) REVERT: C 90 ARG cc_start: 0.6381 (tpt-90) cc_final: 0.6099 (tpp-160) REVERT: C 326 ASN cc_start: 0.7325 (OUTLIER) cc_final: 0.6952 (p0) REVERT: D 128 ILE cc_start: 0.7052 (mm) cc_final: 0.6808 (pt) REVERT: D 195 THR cc_start: 0.7394 (OUTLIER) cc_final: 0.7089 (m) REVERT: Y 131 ASP cc_start: 0.8243 (m-30) cc_final: 0.7955 (m-30) REVERT: Y 240 MET cc_start: 0.5251 (mtm) cc_final: 0.3416 (tpt) REVERT: Z 123 GLN cc_start: 0.6834 (pm20) cc_final: 0.6011 (mp10) REVERT: Z 460 ASP cc_start: 0.5911 (m-30) cc_final: 0.5455 (t0) REVERT: Z 494 PHE cc_start: 0.4243 (t80) cc_final: 0.3104 (m-80) outliers start: 56 outliers final: 40 residues processed: 254 average time/residue: 0.3259 time to fit residues: 129.3106 Evaluate side-chains 225 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 182 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 130 THR Chi-restraints excluded: chain A residue 172 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 292 VAL Chi-restraints excluded: chain A residue 295 SER Chi-restraints excluded: chain A residue 357 MET Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 434 VAL Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 163 MET Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain X residue 442 ILE Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 193 ASP Chi-restraints excluded: chain Z residue 199 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 212 optimal weight: 2.9990 chunk 161 optimal weight: 0.6980 chunk 111 optimal weight: 7.9990 chunk 23 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 144 optimal weight: 0.9990 chunk 215 optimal weight: 4.9990 chunk 228 optimal weight: 0.0000 chunk 112 optimal weight: 1.9990 chunk 204 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 203 GLN ** A 255 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 GLN C 294 ASN ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22551 Z= 0.184 Angle : 0.665 10.951 31216 Z= 0.356 Chirality : 0.042 0.187 3516 Planarity : 0.005 0.063 3379 Dihedral : 24.107 179.501 4372 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.13 % Allowed : 12.82 % Favored : 87.04 % Rotamer: Outliers : 2.49 % Allowed : 18.21 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.17), residues: 2223 helix: 0.07 (0.18), residues: 857 sheet: -2.15 (0.45), residues: 96 loop : -2.80 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP Z 213 HIS 0.008 0.001 HIS D 122 PHE 0.030 0.002 PHE C 506 TYR 0.019 0.001 TYR D 235 ARG 0.006 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 208 time to evaluate : 2.466 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: B 283 HIS cc_start: 0.6776 (p-80) cc_final: 0.6362 (p-80) REVERT: B 390 MET cc_start: 0.6079 (ptt) cc_final: 0.5785 (mtt) REVERT: C 71 MET cc_start: 0.3870 (mmm) cc_final: 0.3303 (mmt) REVERT: C 90 ARG cc_start: 0.6441 (tpt-90) cc_final: 0.6136 (tpp-160) REVERT: C 280 GLN cc_start: 0.5465 (tp40) cc_final: 0.5253 (mm-40) REVERT: C 326 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.6921 (p0) REVERT: D 128 ILE cc_start: 0.7206 (mm) cc_final: 0.6990 (pt) REVERT: Y 97 LYS cc_start: 0.5834 (mttt) cc_final: 0.4706 (pttm) REVERT: Y 121 MET cc_start: 0.5002 (tpt) cc_final: 0.4705 (tpp) REVERT: Y 131 ASP cc_start: 0.8174 (m-30) cc_final: 0.7918 (m-30) REVERT: Y 240 MET cc_start: 0.5107 (mtm) cc_final: 0.3347 (tpt) REVERT: Z 214 MET cc_start: 0.5677 (ttm) cc_final: 0.4040 (mtp) REVERT: Z 460 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5548 (t0) REVERT: Z 494 PHE cc_start: 0.4636 (t80) cc_final: 0.2904 (m-80) outliers start: 50 outliers final: 31 residues processed: 244 average time/residue: 0.3373 time to fit residues: 127.7540 Evaluate side-chains 226 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 193 time to evaluate : 2.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 117 TRP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 74 TYR Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 460 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 189 optimal weight: 7.9990 chunk 129 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 169 optimal weight: 3.9990 chunk 94 optimal weight: 5.9990 chunk 194 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 116 optimal weight: 0.7980 chunk 204 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 GLN A 428 GLN B 31 HIS B 85 GLN ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6310 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 22551 Z= 0.217 Angle : 0.674 9.822 31216 Z= 0.361 Chirality : 0.043 0.179 3516 Planarity : 0.005 0.062 3379 Dihedral : 24.141 179.260 4372 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.81 % Favored : 86.05 % Rotamer: Outliers : 3.23 % Allowed : 18.96 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.29 (0.17), residues: 2223 helix: 0.10 (0.18), residues: 860 sheet: -1.96 (0.45), residues: 102 loop : -2.81 (0.17), residues: 1261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.003 TRP Z 213 HIS 0.010 0.001 HIS B 95 PHE 0.021 0.002 PHE A 213 TYR 0.027 0.002 TYR B 435 ARG 0.006 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 205 time to evaluate : 2.127 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 45 MET cc_start: 0.6674 (mmp) cc_final: 0.5758 (mtp) REVERT: A 163 MET cc_start: 0.6095 (mmm) cc_final: 0.5791 (mtp) REVERT: B 161 ILE cc_start: 0.5312 (OUTLIER) cc_final: 0.4980 (tt) REVERT: B 390 MET cc_start: 0.6089 (ptt) cc_final: 0.5745 (mtt) REVERT: C 71 MET cc_start: 0.3752 (mmm) cc_final: 0.3159 (mmt) REVERT: C 90 ARG cc_start: 0.6459 (tpt-90) cc_final: 0.6203 (tpp-160) REVERT: C 326 ASN cc_start: 0.7396 (OUTLIER) cc_final: 0.6915 (p0) REVERT: D 31 HIS cc_start: 0.5763 (OUTLIER) cc_final: 0.5084 (t-90) REVERT: D 117 TRP cc_start: 0.6961 (OUTLIER) cc_final: 0.6331 (t60) REVERT: D 128 ILE cc_start: 0.7068 (mm) cc_final: 0.6432 (tp) REVERT: D 169 LEU cc_start: 0.7632 (OUTLIER) cc_final: 0.7431 (mt) REVERT: D 195 THR cc_start: 0.7350 (OUTLIER) cc_final: 0.7076 (m) REVERT: Y 121 MET cc_start: 0.5143 (tpt) cc_final: 0.4853 (tpp) REVERT: Y 131 ASP cc_start: 0.8157 (m-30) cc_final: 0.7899 (m-30) REVERT: Y 240 MET cc_start: 0.5059 (mtm) cc_final: 0.3185 (tpt) REVERT: Z 214 MET cc_start: 0.5955 (ttm) cc_final: 0.4589 (mtp) outliers start: 65 outliers final: 45 residues processed: 252 average time/residue: 0.3601 time to fit residues: 141.8656 Evaluate side-chains 231 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 180 time to evaluate : 2.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 117 TRP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 202 THR Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 107 THR Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain X residue 442 ILE Chi-restraints excluded: chain Y residue 84 THR Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 153 SER Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 460 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 76 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 133 optimal weight: 8.9990 chunk 56 optimal weight: 4.9990 chunk 228 optimal weight: 0.0770 chunk 189 optimal weight: 10.0000 chunk 105 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.1740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 349 GLN ** C 474 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 476 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 22551 Z= 0.201 Angle : 0.672 13.316 31216 Z= 0.360 Chirality : 0.042 0.186 3516 Planarity : 0.005 0.062 3379 Dihedral : 24.101 179.169 4370 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.15 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.41 % Favored : 86.46 % Rotamer: Outliers : 3.38 % Allowed : 19.35 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.17), residues: 2223 helix: 0.15 (0.18), residues: 855 sheet: -2.04 (0.45), residues: 102 loop : -2.80 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.078 0.003 TRP Z 213 HIS 0.008 0.001 HIS B 95 PHE 0.025 0.002 PHE D 186 TYR 0.028 0.002 TYR B 435 ARG 0.005 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 200 time to evaluate : 2.234 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 163 MET cc_start: 0.5854 (mmm) cc_final: 0.5615 (mtp) REVERT: B 161 ILE cc_start: 0.5295 (OUTLIER) cc_final: 0.4960 (tt) REVERT: B 390 MET cc_start: 0.6112 (ptt) cc_final: 0.5838 (mtt) REVERT: C 71 MET cc_start: 0.3809 (mmm) cc_final: 0.3107 (mmt) REVERT: C 90 ARG cc_start: 0.6528 (tpt-90) cc_final: 0.6286 (tpp-160) REVERT: C 326 ASN cc_start: 0.7426 (OUTLIER) cc_final: 0.6940 (p0) REVERT: C 425 ILE cc_start: 0.7287 (OUTLIER) cc_final: 0.7018 (tp) REVERT: C 475 MET cc_start: 0.6393 (mmm) cc_final: 0.6124 (mmm) REVERT: D 31 HIS cc_start: 0.5431 (OUTLIER) cc_final: 0.4556 (t-90) REVERT: D 117 TRP cc_start: 0.7046 (OUTLIER) cc_final: 0.6471 (t60) REVERT: D 127 TYR cc_start: 0.6801 (t80) cc_final: 0.6583 (t80) REVERT: D 128 ILE cc_start: 0.7089 (mm) cc_final: 0.6573 (tp) REVERT: D 137 ILE cc_start: 0.4377 (OUTLIER) cc_final: 0.4117 (tt) REVERT: D 169 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7522 (mt) REVERT: D 195 THR cc_start: 0.7361 (OUTLIER) cc_final: 0.7108 (m) REVERT: Y 121 MET cc_start: 0.5083 (tpt) cc_final: 0.4862 (tpp) REVERT: Y 131 ASP cc_start: 0.8126 (m-30) cc_final: 0.7873 (m-30) REVERT: Y 240 MET cc_start: 0.5093 (mtm) cc_final: 0.3339 (tpt) REVERT: Z 123 GLN cc_start: 0.6972 (pm20) cc_final: 0.5939 (mp10) REVERT: Z 155 TYR cc_start: 0.5777 (OUTLIER) cc_final: 0.5500 (m-80) REVERT: Z 214 MET cc_start: 0.5958 (ttm) cc_final: 0.4527 (mtp) REVERT: Z 494 PHE cc_start: 0.3919 (t80) cc_final: 0.3233 (m-10) outliers start: 68 outliers final: 46 residues processed: 252 average time/residue: 0.3260 time to fit residues: 128.6891 Evaluate side-chains 243 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 188 time to evaluate : 2.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 117 TRP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 225 ASP Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 349 GLN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 169 LEU Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain Y residue 114 LEU Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 94 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 154 VAL Chi-restraints excluded: chain Z residue 155 TYR Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 193 ASP Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 460 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 220 optimal weight: 10.0000 chunk 25 optimal weight: 0.0470 chunk 130 optimal weight: 0.7980 chunk 166 optimal weight: 0.8980 chunk 129 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 127 optimal weight: 0.8980 chunk 227 optimal weight: 0.8980 chunk 142 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 349 GLN C 474 HIS ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.3167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 22551 Z= 0.179 Angle : 0.664 13.298 31216 Z= 0.352 Chirality : 0.041 0.183 3516 Planarity : 0.005 0.072 3379 Dihedral : 24.072 178.658 4370 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 13.50 % Favored : 86.37 % Rotamer: Outliers : 3.33 % Allowed : 19.85 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.18), residues: 2223 helix: 0.16 (0.18), residues: 861 sheet: -2.29 (0.44), residues: 96 loop : -2.79 (0.17), residues: 1266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.086 0.003 TRP Z 213 HIS 0.008 0.001 HIS D 122 PHE 0.021 0.002 PHE B 209 TYR 0.024 0.001 TYR B 435 ARG 0.008 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 198 time to evaluate : 2.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 ILE cc_start: 0.5270 (OUTLIER) cc_final: 0.4931 (tt) REVERT: B 390 MET cc_start: 0.6096 (ptt) cc_final: 0.5839 (mtt) REVERT: C 90 ARG cc_start: 0.6474 (tpt-90) cc_final: 0.6226 (tpp-160) REVERT: C 326 ASN cc_start: 0.7419 (OUTLIER) cc_final: 0.6896 (p0) REVERT: C 425 ILE cc_start: 0.7233 (OUTLIER) cc_final: 0.6982 (tp) REVERT: D 31 HIS cc_start: 0.5305 (OUTLIER) cc_final: 0.4454 (t-90) REVERT: D 117 TRP cc_start: 0.6959 (OUTLIER) cc_final: 0.6333 (t60) REVERT: D 127 TYR cc_start: 0.6800 (t80) cc_final: 0.6551 (t80) REVERT: D 128 ILE cc_start: 0.7084 (mm) cc_final: 0.6636 (tp) REVERT: D 137 ILE cc_start: 0.4351 (OUTLIER) cc_final: 0.4071 (tt) REVERT: D 155 GLU cc_start: 0.5984 (tp30) cc_final: 0.5747 (tp30) REVERT: D 195 THR cc_start: 0.7412 (OUTLIER) cc_final: 0.7105 (m) REVERT: Y 121 MET cc_start: 0.5085 (tpt) cc_final: 0.4852 (tpp) REVERT: Y 131 ASP cc_start: 0.8132 (m-30) cc_final: 0.7886 (m-30) REVERT: Y 240 MET cc_start: 0.5165 (mtm) cc_final: 0.3414 (tpt) REVERT: Z 123 GLN cc_start: 0.6885 (pm20) cc_final: 0.5911 (mp10) REVERT: Z 155 TYR cc_start: 0.5821 (OUTLIER) cc_final: 0.5483 (m-80) REVERT: Z 214 MET cc_start: 0.5889 (ttm) cc_final: 0.4544 (mtp) REVERT: Z 494 PHE cc_start: 0.3864 (t80) cc_final: 0.3344 (m-10) outliers start: 67 outliers final: 46 residues processed: 248 average time/residue: 0.3237 time to fit residues: 125.7839 Evaluate side-chains 242 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 188 time to evaluate : 2.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 117 TRP Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 215 TYR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain B residue 490 GLU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 290 GLU Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 117 TRP Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 94 LEU Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 150 LEU Chi-restraints excluded: chain Z residue 153 SER Chi-restraints excluded: chain Z residue 155 TYR Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 193 ASP Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 460 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 140 optimal weight: 0.1980 chunk 90 optimal weight: 0.9990 chunk 135 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 144 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 112 optimal weight: 0.0470 chunk 21 optimal weight: 0.7980 chunk 178 optimal weight: 7.9990 chunk 206 optimal weight: 0.0770 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 288 GLN A 315 ASN B 85 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.3250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22551 Z= 0.167 Angle : 0.661 13.323 31216 Z= 0.350 Chirality : 0.041 0.177 3516 Planarity : 0.005 0.071 3379 Dihedral : 24.016 179.597 4370 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 16.94 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.78 % Favored : 87.13 % Rotamer: Outliers : 2.64 % Allowed : 20.90 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.18), residues: 2223 helix: 0.19 (0.18), residues: 863 sheet: -2.31 (0.44), residues: 96 loop : -2.76 (0.17), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.002 TRP Z 213 HIS 0.009 0.001 HIS D 122 PHE 0.024 0.001 PHE B 209 TYR 0.027 0.001 TYR C 435 ARG 0.008 0.000 ARG C 269 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 209 time to evaluate : 2.307 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: B 161 ILE cc_start: 0.5285 (OUTLIER) cc_final: 0.4893 (tt) REVERT: B 390 MET cc_start: 0.6004 (ptt) cc_final: 0.5716 (mtt) REVERT: C 90 ARG cc_start: 0.6483 (tpt-90) cc_final: 0.6198 (tpp-160) REVERT: C 178 MET cc_start: 0.6002 (tpt) cc_final: 0.5800 (tpt) REVERT: C 326 ASN cc_start: 0.7454 (OUTLIER) cc_final: 0.6890 (p0) REVERT: C 425 ILE cc_start: 0.7215 (OUTLIER) cc_final: 0.6961 (tp) REVERT: C 475 MET cc_start: 0.6415 (mmm) cc_final: 0.6007 (mmm) REVERT: D 31 HIS cc_start: 0.5214 (OUTLIER) cc_final: 0.4199 (t-90) REVERT: D 127 TYR cc_start: 0.6810 (t80) cc_final: 0.6606 (t80) REVERT: D 128 ILE cc_start: 0.7043 (mm) cc_final: 0.6698 (tp) REVERT: D 137 ILE cc_start: 0.4440 (OUTLIER) cc_final: 0.4130 (tt) REVERT: D 195 THR cc_start: 0.7436 (OUTLIER) cc_final: 0.7092 (m) REVERT: Y 98 ARG cc_start: 0.5869 (ptm160) cc_final: 0.5494 (ttm-80) REVERT: Y 121 MET cc_start: 0.5079 (tpt) cc_final: 0.4834 (tpp) REVERT: Y 131 ASP cc_start: 0.8140 (m-30) cc_final: 0.7894 (m-30) REVERT: Y 240 MET cc_start: 0.5135 (mtm) cc_final: 0.3356 (tpt) REVERT: Z 112 LEU cc_start: 0.6993 (OUTLIER) cc_final: 0.6691 (mt) REVERT: Z 155 TYR cc_start: 0.5858 (OUTLIER) cc_final: 0.5479 (m-80) REVERT: Z 214 MET cc_start: 0.5866 (ttm) cc_final: 0.4515 (mtp) REVERT: Z 460 ASP cc_start: 0.5925 (OUTLIER) cc_final: 0.5554 (t0) REVERT: Z 494 PHE cc_start: 0.4054 (t80) cc_final: 0.3524 (m-10) outliers start: 53 outliers final: 34 residues processed: 249 average time/residue: 0.3337 time to fit residues: 129.8705 Evaluate side-chains 228 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 185 time to evaluate : 2.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TRP Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain D residue 346 THR Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 94 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 153 SER Chi-restraints excluded: chain Z residue 155 TYR Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 193 ASP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 460 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 217 optimal weight: 0.0770 chunk 198 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 127 optimal weight: 2.9990 chunk 92 optimal weight: 0.9990 chunk 166 optimal weight: 0.9980 chunk 65 optimal weight: 0.0170 chunk 191 optimal weight: 4.9990 chunk 200 optimal weight: 5.9990 chunk 139 optimal weight: 0.8980 chunk 224 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6236 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22551 Z= 0.173 Angle : 0.677 12.965 31216 Z= 0.353 Chirality : 0.042 0.383 3516 Planarity : 0.005 0.072 3379 Dihedral : 24.029 179.924 4370 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.14 % Favored : 86.77 % Rotamer: Outliers : 2.64 % Allowed : 21.64 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.18), residues: 2223 helix: 0.24 (0.18), residues: 863 sheet: -2.05 (0.45), residues: 102 loop : -2.74 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP Z 213 HIS 0.008 0.001 HIS D 122 PHE 0.040 0.002 PHE D 291 TYR 0.022 0.001 TYR C 274 ARG 0.010 0.000 ARG Y 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 194 time to evaluate : 2.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 161 ILE cc_start: 0.5213 (OUTLIER) cc_final: 0.4873 (tt) REVERT: B 390 MET cc_start: 0.6011 (ptt) cc_final: 0.5768 (mtt) REVERT: C 90 ARG cc_start: 0.6502 (tpt-90) cc_final: 0.6250 (tpp-160) REVERT: C 326 ASN cc_start: 0.7612 (OUTLIER) cc_final: 0.7072 (p0) REVERT: C 425 ILE cc_start: 0.7166 (OUTLIER) cc_final: 0.6871 (tp) REVERT: D 31 HIS cc_start: 0.5134 (OUTLIER) cc_final: 0.4149 (t-90) REVERT: D 32 MET cc_start: 0.6620 (ptp) cc_final: 0.6113 (ptt) REVERT: D 127 TYR cc_start: 0.6905 (t80) cc_final: 0.6666 (t80) REVERT: D 128 ILE cc_start: 0.7062 (mm) cc_final: 0.6653 (tp) REVERT: D 137 ILE cc_start: 0.4386 (OUTLIER) cc_final: 0.4088 (tt) REVERT: D 195 THR cc_start: 0.7400 (OUTLIER) cc_final: 0.7047 (m) REVERT: Y 121 MET cc_start: 0.5104 (tpt) cc_final: 0.4900 (tpp) REVERT: Y 131 ASP cc_start: 0.8069 (m-30) cc_final: 0.7842 (m-30) REVERT: Y 240 MET cc_start: 0.5119 (mtm) cc_final: 0.3328 (tpt) REVERT: Z 112 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6769 (mt) REVERT: Z 155 TYR cc_start: 0.5838 (OUTLIER) cc_final: 0.5480 (m-80) REVERT: Z 214 MET cc_start: 0.5930 (ttm) cc_final: 0.4575 (mtp) REVERT: Z 460 ASP cc_start: 0.5941 (OUTLIER) cc_final: 0.5549 (t0) REVERT: Z 494 PHE cc_start: 0.3983 (t80) cc_final: 0.3500 (m-10) outliers start: 53 outliers final: 37 residues processed: 235 average time/residue: 0.3142 time to fit residues: 117.2724 Evaluate side-chains 231 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 185 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 TRP Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 306 PHE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain D residue 323 ASP Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 94 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 153 SER Chi-restraints excluded: chain Z residue 155 TYR Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 193 ASP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 460 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 136 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 155 optimal weight: 9.9990 chunk 235 optimal weight: 3.9990 chunk 216 optimal weight: 0.0000 chunk 187 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 148 optimal weight: 7.9990 chunk 199 optimal weight: 0.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6246 moved from start: 0.3453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 22551 Z= 0.179 Angle : 0.673 12.189 31216 Z= 0.352 Chirality : 0.041 0.302 3516 Planarity : 0.005 0.061 3379 Dihedral : 24.047 179.856 4370 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.27 % Favored : 86.64 % Rotamer: Outliers : 2.39 % Allowed : 21.99 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.18), residues: 2223 helix: 0.28 (0.18), residues: 863 sheet: -2.04 (0.45), residues: 102 loop : -2.74 (0.17), residues: 1258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP Z 213 HIS 0.012 0.001 HIS Z 184 PHE 0.037 0.002 PHE D 291 TYR 0.024 0.001 TYR C 435 ARG 0.008 0.000 ARG Y 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4446 Ramachandran restraints generated. 2223 Oldfield, 0 Emsley, 2223 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 191 time to evaluate : 2.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 LEU cc_start: 0.6429 (mp) cc_final: 0.5852 (mt) REVERT: B 161 ILE cc_start: 0.5230 (OUTLIER) cc_final: 0.4892 (tt) REVERT: C 90 ARG cc_start: 0.6312 (tpt-90) cc_final: 0.6075 (tpp-160) REVERT: C 326 ASN cc_start: 0.7603 (OUTLIER) cc_final: 0.7077 (p0) REVERT: C 425 ILE cc_start: 0.7171 (OUTLIER) cc_final: 0.6857 (tp) REVERT: D 31 HIS cc_start: 0.5042 (OUTLIER) cc_final: 0.4006 (t-90) REVERT: D 32 MET cc_start: 0.6595 (ptp) cc_final: 0.6105 (ptt) REVERT: D 127 TYR cc_start: 0.6911 (t80) cc_final: 0.6672 (t80) REVERT: D 128 ILE cc_start: 0.7060 (mm) cc_final: 0.6670 (tp) REVERT: D 137 ILE cc_start: 0.4389 (OUTLIER) cc_final: 0.4168 (tt) REVERT: D 195 THR cc_start: 0.7373 (OUTLIER) cc_final: 0.7028 (m) REVERT: Y 131 ASP cc_start: 0.8036 (m-30) cc_final: 0.7797 (m-30) REVERT: Y 240 MET cc_start: 0.5155 (mtm) cc_final: 0.3387 (tpt) REVERT: Z 112 LEU cc_start: 0.7048 (OUTLIER) cc_final: 0.6751 (mt) REVERT: Z 155 TYR cc_start: 0.5859 (OUTLIER) cc_final: 0.5532 (m-80) REVERT: Z 214 MET cc_start: 0.5844 (ttm) cc_final: 0.4563 (mtp) REVERT: Z 460 ASP cc_start: 0.5902 (OUTLIER) cc_final: 0.5524 (t0) REVERT: Z 494 PHE cc_start: 0.3859 (t80) cc_final: 0.3451 (m-10) outliers start: 48 outliers final: 37 residues processed: 229 average time/residue: 0.3086 time to fit residues: 112.3982 Evaluate side-chains 228 residues out of total 2047 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 182 time to evaluate : 2.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 117 TRP Chi-restraints excluded: chain A residue 213 PHE Chi-restraints excluded: chain A residue 223 THR Chi-restraints excluded: chain A residue 228 VAL Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 385 LYS Chi-restraints excluded: chain A residue 397 VAL Chi-restraints excluded: chain B residue 117 TRP Chi-restraints excluded: chain B residue 132 VAL Chi-restraints excluded: chain B residue 153 ILE Chi-restraints excluded: chain B residue 161 ILE Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 181 VAL Chi-restraints excluded: chain B residue 182 VAL Chi-restraints excluded: chain B residue 208 LEU Chi-restraints excluded: chain B residue 213 PHE Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 473 CYS Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 200 ASP Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 231 THR Chi-restraints excluded: chain C residue 319 ILE Chi-restraints excluded: chain C residue 326 ASN Chi-restraints excluded: chain C residue 395 ILE Chi-restraints excluded: chain C residue 425 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 31 HIS Chi-restraints excluded: chain D residue 124 ILE Chi-restraints excluded: chain D residue 137 ILE Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain D residue 198 THR Chi-restraints excluded: chain D residue 213 PHE Chi-restraints excluded: chain D residue 231 THR Chi-restraints excluded: chain Y residue 188 GLU Chi-restraints excluded: chain Z residue 94 LEU Chi-restraints excluded: chain Z residue 112 LEU Chi-restraints excluded: chain Z residue 153 SER Chi-restraints excluded: chain Z residue 155 TYR Chi-restraints excluded: chain Z residue 157 ILE Chi-restraints excluded: chain Z residue 193 ASP Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 199 VAL Chi-restraints excluded: chain Z residue 460 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 236 random chunks: chunk 57 optimal weight: 2.9990 chunk 172 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 187 optimal weight: 7.9990 chunk 78 optimal weight: 0.6980 chunk 192 optimal weight: 10.0000 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 164 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 379 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 393 GLN ** C 265 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 349 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 354 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.115360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.095579 restraints weight = 86428.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.095677 restraints weight = 59150.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.096062 restraints weight = 46212.863| |-----------------------------------------------------------------------------| r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6429 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22551 Z= 0.197 Angle : 0.687 14.967 31216 Z= 0.358 Chirality : 0.042 0.183 3516 Planarity : 0.005 0.072 3379 Dihedral : 24.079 179.550 4370 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.09 % Allowed : 13.54 % Favored : 86.37 % Rotamer: Outliers : 2.89 % Allowed : 21.64 % Favored : 75.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.14 (0.18), residues: 2223 helix: 0.25 (0.18), residues: 861 sheet: -2.08 (0.45), residues: 102 loop : -2.73 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP Z 213 HIS 0.011 0.001 HIS Z 184 PHE 0.035 0.002 PHE D 291 TYR 0.020 0.001 TYR B 435 ARG 0.009 0.000 ARG Y 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3948.10 seconds wall clock time: 73 minutes 49.40 seconds (4429.40 seconds total)