Starting phenix.real_space_refine on Mon Mar 11 08:58:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/03_2024/7dhi_30681_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/03_2024/7dhi_30681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/03_2024/7dhi_30681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/03_2024/7dhi_30681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/03_2024/7dhi_30681_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7dhi_30681/03_2024/7dhi_30681_updated.pdb" } resolution = 3.26 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 4990 2.51 5 N 1341 2.21 5 O 1420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 33": "OD1" <-> "OD2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 344": "OE1" <-> "OE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ASP 20": "OD1" <-> "OD2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 153": "OD1" <-> "OD2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 17": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N ASP 73": "OD1" <-> "OD2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 113": "OD1" <-> "OD2" Residue "R TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 192": "OD1" <-> "OD2" Residue "R PHE 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 194": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 225": "OE1" <-> "OE2" Residue "R GLU 237": "OE1" <-> "OE2" Residue "R PHE 290": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7799 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1692 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 4 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 4, 'ASP:plan': 7} Unresolved non-hydrogen planarities: 85 Chain: "B" Number of atoms: 2497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2497 Classifications: {'peptide': 335} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 329} Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 63 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "G" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 377 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 47} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 32 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "N" Number of atoms: 952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 952 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "R" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2279 Unusual residues: {'68H': 1} Classifications: {'peptide': 290, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 7, 'TRANS': 282, None: 1} Not linked: pdbres="CYS R 341 " pdbres="68H R 401 " Chain breaks: 1 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 61 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 4.91, per 1000 atoms: 0.63 Number of scatterers: 7799 At special positions: 0 Unit cell: (91.26, 95.316, 129.792, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 48 16.00 O 1420 8.00 N 1341 7.00 C 4990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 106 " - pdb=" SG CYS R 191 " 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: 2.90 Conformation dependent library (CDL) restraints added in 1.3 seconds 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 31 helices and 11 sheets defined 32.2% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 13 through 37 removed outlier: 3.576A pdb=" N ILE A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 265 through 276 removed outlier: 3.632A pdb=" N ALA A 269 " --> pdb=" O ARG A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 301 Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.815A pdb=" N ILE A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 342 " --> pdb=" O LYS A 338 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 390 removed outlier: 4.147A pdb=" N ILE A 372 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ARG A 373 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG A 374 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 377 " --> pdb=" O ARG A 374 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N CYS A 379 " --> pdb=" O PHE A 376 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG A 380 " --> pdb=" O ASN A 377 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 383 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLN A 384 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 385 " --> pdb=" O ILE A 382 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU A 388 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 389 " --> pdb=" O MET A 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 25 removed outlier: 3.559A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.842A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 21 removed outlier: 3.565A pdb=" N GLU G 17 " --> pdb=" O ARG G 13 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLN G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N MET G 21 " --> pdb=" O GLU G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.759A pdb=" N TYR G 40 " --> pdb=" O ASP G 36 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N CYS G 41 " --> pdb=" O LEU G 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 32 through 39 removed outlier: 3.520A pdb=" N ILE R 38 " --> pdb=" O VAL R 34 " (cutoff:3.500A) Processing helix chain 'R' and resid 41 through 50 removed outlier: 3.923A pdb=" N PHE R 49 " --> pdb=" O LEU R 45 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLY R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 52 through 58 removed outlier: 3.784A pdb=" N ALA R 57 " --> pdb=" O LEU R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 68 through 85 removed outlier: 3.755A pdb=" N ILE R 72 " --> pdb=" O THR R 68 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL R 77 " --> pdb=" O THR R 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU R 80 " --> pdb=" O ALA R 76 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N MET R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 96 Processing helix chain 'R' and resid 106 through 136 removed outlier: 3.500A pdb=" N SER R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE R 135 " --> pdb=" O ARG R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 138 through 140 No H-bonds generated for 'chain 'R' and resid 138 through 140' Processing helix chain 'R' and resid 150 through 160 Processing helix chain 'R' and resid 167 through 170 No H-bonds generated for 'chain 'R' and resid 167 through 170' Processing helix chain 'R' and resid 202 through 207 Processing helix chain 'R' and resid 209 through 219 removed outlier: 3.577A pdb=" N TYR R 219 " --> pdb=" O MET R 215 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 236 removed outlier: 4.083A pdb=" N ARG R 228 " --> pdb=" O GLN R 224 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP R 234 " --> pdb=" O LEU R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 273 No H-bonds generated for 'chain 'R' and resid 270 through 273' Processing helix chain 'R' and resid 275 through 292 removed outlier: 3.751A pdb=" N MET R 279 " --> pdb=" O LEU R 275 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N THR R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR R 283 " --> pdb=" O MET R 279 " (cutoff:3.500A) Proline residue: R 288 - end of helix removed outlier: 4.013A pdb=" N VAL R 292 " --> pdb=" O PRO R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 307 through 313 Processing helix chain 'R' and resid 317 through 325 removed outlier: 4.759A pdb=" N ASN R 322 " --> pdb=" O SER R 319 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 330 through 339 Processing sheet with id= A, first strand: chain 'A' and resid 40 through 45 removed outlier: 6.991A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.098A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.714A pdb=" N SER A 286 " --> pdb=" O ILE A 244 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.078A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.848A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.272A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.285A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 166 through 170 removed outlier: 3.707A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 232 removed outlier: 7.180A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.908A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.888A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.710A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 208 through 211 removed outlier: 3.872A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.786A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR N 78 " --> pdb=" O ASP N 73 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.676A pdb=" N THR N 122 " --> pdb=" O TYR N 94 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER N 59 " --> pdb=" O ASP N 50 " (cutoff:3.500A) 245 hydrogen bonds defined for protein. 666 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 3.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2504 1.34 - 1.46: 1921 1.46 - 1.58: 3468 1.58 - 1.70: 0 1.70 - 1.82: 67 Bond restraints: 7960 Sorted by residual: bond pdb=" CA THR A 263 " pdb=" CB THR A 263 " ideal model delta sigma weight residual 1.530 1.552 -0.022 1.69e-02 3.50e+03 1.68e+00 bond pdb=" C VAL R 87 " pdb=" N PRO R 88 " ideal model delta sigma weight residual 1.336 1.351 -0.016 1.23e-02 6.61e+03 1.64e+00 bond pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta sigma weight residual 1.458 1.480 -0.022 1.77e-02 3.19e+03 1.52e+00 bond pdb=" CB PRO R 211 " pdb=" CG PRO R 211 " ideal model delta sigma weight residual 1.492 1.431 0.061 5.00e-02 4.00e+02 1.48e+00 bond pdb=" N THR A 263 " pdb=" CA THR A 263 " ideal model delta sigma weight residual 1.457 1.473 -0.016 1.29e-02 6.01e+03 1.47e+00 ... (remaining 7955 not shown) Histogram of bond angle deviations from ideal: 100.31 - 107.08: 183 107.08 - 113.85: 4451 113.85 - 120.63: 3242 120.63 - 127.40: 2860 127.40 - 134.18: 90 Bond angle restraints: 10826 Sorted by residual: angle pdb=" N VAL R 31 " pdb=" CA VAL R 31 " pdb=" C VAL R 31 " ideal model delta sigma weight residual 113.53 109.05 4.48 9.80e-01 1.04e+00 2.09e+01 angle pdb=" C GLN A 262 " pdb=" N THR A 263 " pdb=" CA THR A 263 " ideal model delta sigma weight residual 121.54 129.98 -8.44 1.91e+00 2.74e-01 1.95e+01 angle pdb=" C ASP N 109 " pdb=" N VAL N 110 " pdb=" CA VAL N 110 " ideal model delta sigma weight residual 121.97 129.33 -7.36 1.80e+00 3.09e-01 1.67e+01 angle pdb=" C GLY R 238 " pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta sigma weight residual 125.66 133.15 -7.49 1.85e+00 2.92e-01 1.64e+01 angle pdb=" C HIS R 241 " pdb=" N VAL R 242 " pdb=" CA VAL R 242 " ideal model delta sigma weight residual 121.70 128.26 -6.56 1.80e+00 3.09e-01 1.33e+01 ... (remaining 10821 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.97: 4152 16.97 - 33.95: 421 33.95 - 50.92: 74 50.92 - 67.90: 13 67.90 - 84.87: 9 Dihedral angle restraints: 4669 sinusoidal: 1706 harmonic: 2963 Sorted by residual: dihedral pdb=" CA HIS R 178 " pdb=" C HIS R 178 " pdb=" N GLN R 179 " pdb=" CA GLN R 179 " ideal model delta harmonic sigma weight residual -180.00 -147.15 -32.85 0 5.00e+00 4.00e-02 4.32e+01 dihedral pdb=" CA GLY R 238 " pdb=" C GLY R 238 " pdb=" N ARG R 239 " pdb=" CA ARG R 239 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA THR R 177 " pdb=" C THR R 177 " pdb=" N HIS R 178 " pdb=" CA HIS R 178 " ideal model delta harmonic sigma weight residual 180.00 -152.95 -27.05 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 4666 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 878 0.049 - 0.097: 292 0.097 - 0.146: 76 0.146 - 0.195: 8 0.195 - 0.244: 1 Chirality restraints: 1255 Sorted by residual: chirality pdb=" CB VAL A 241 " pdb=" CA VAL A 241 " pdb=" CG1 VAL A 241 " pdb=" CG2 VAL A 241 " both_signs ideal model delta sigma weight residual False -2.63 -2.39 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA THR A 263 " pdb=" N THR A 263 " pdb=" C THR A 263 " pdb=" CB THR A 263 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CB THR A 320 " pdb=" CA THR A 320 " pdb=" OG1 THR A 320 " pdb=" CG2 THR A 320 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.10e-01 ... (remaining 1252 not shown) Planarity restraints: 1367 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 322 " -0.048 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO R 323 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 323 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO R 323 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " -0.040 5.00e-02 4.00e+02 6.09e-02 5.94e+00 pdb=" N PRO N 88 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 210 " -0.040 5.00e-02 4.00e+02 5.87e-02 5.52e+00 pdb=" N PRO R 211 " 0.102 5.00e-02 4.00e+02 pdb=" CA PRO R 211 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 211 " -0.033 5.00e-02 4.00e+02 ... (remaining 1364 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2468 2.82 - 3.34: 6404 3.34 - 3.86: 12385 3.86 - 4.38: 14729 4.38 - 4.90: 25410 Nonbonded interactions: 61396 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.298 2.440 nonbonded pdb=" O ALA R 119 " pdb=" OG1 THR R 123 " model vdw 2.298 2.440 nonbonded pdb=" OG SER B 227 " pdb=" O PRO N 100 " model vdw 2.303 2.440 nonbonded pdb=" OG SER R 203 " pdb=" O2 68H R 401 " model vdw 2.306 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.308 2.440 ... (remaining 61391 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.370 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.770 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 0.061 7960 Z= 0.253 Angle : 0.762 8.765 10826 Z= 0.424 Chirality : 0.051 0.244 1255 Planarity : 0.006 0.071 1367 Dihedral : 14.529 84.870 2743 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 4.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.13 % Allowed : 8.77 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -5.36 (0.19), residues: 999 helix: -4.75 (0.09), residues: 351 sheet: -2.28 (0.32), residues: 227 loop : -2.99 (0.24), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.017 0.002 PHE B 199 TYR 0.017 0.001 TYR B 59 ARG 0.003 0.000 ARG N 72 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 200 time to evaluate : 0.849 Fit side-chains REVERT: A 16 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7775 (tt0) REVERT: A 236 GLN cc_start: 0.8367 (pt0) cc_final: 0.8074 (pt0) REVERT: A 336 ARG cc_start: 0.8162 (ttt-90) cc_final: 0.7849 (ttt180) REVERT: A 343 ASP cc_start: 0.7752 (m-30) cc_final: 0.7545 (m-30) REVERT: B 308 LEU cc_start: 0.8714 (pp) cc_final: 0.8496 (pt) REVERT: N 87 LYS cc_start: 0.8764 (ttmt) cc_final: 0.8286 (mmtp) REVERT: N 118 ARG cc_start: 0.8493 (ttp-170) cc_final: 0.8272 (ttm170) REVERT: N 123 GLN cc_start: 0.8647 (tp40) cc_final: 0.8413 (tp40) REVERT: R 40 MET cc_start: 0.7860 (mtm) cc_final: 0.7501 (mtt) REVERT: R 224 GLN cc_start: 0.7392 (mt0) cc_final: 0.6990 (tm-30) outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2405 time to fit residues: 61.5777 Evaluate side-chains 160 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 5.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 47 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 90 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 29 GLN A 213 GLN A 218 ASN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 227 GLN B 32 GLN B 88 ASN B 142 HIS B 156 GLN B 239 ASN B 340 ASN N 3 GLN N 39 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.055 7960 Z= 0.491 Angle : 0.674 7.140 10826 Z= 0.365 Chirality : 0.047 0.158 1255 Planarity : 0.005 0.054 1367 Dihedral : 6.850 86.275 1102 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.01 % Favored : 92.99 % Rotamer: Outliers : 2.88 % Allowed : 17.92 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.95 (0.22), residues: 999 helix: -2.76 (0.21), residues: 355 sheet: -1.88 (0.32), residues: 230 loop : -2.77 (0.26), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 109 HIS 0.009 0.002 HIS A 357 PHE 0.016 0.002 PHE B 234 TYR 0.026 0.002 TYR B 59 ARG 0.009 0.001 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 1.157 Fit side-chains revert: symmetry clash REVERT: B 63 TRP cc_start: 0.8431 (OUTLIER) cc_final: 0.8004 (t-100) REVERT: B 75 GLN cc_start: 0.8931 (mt0) cc_final: 0.8685 (mm-40) REVERT: B 234 PHE cc_start: 0.9008 (OUTLIER) cc_final: 0.7937 (t80) REVERT: N 18 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7708 (tt) REVERT: N 87 LYS cc_start: 0.8778 (ttmt) cc_final: 0.8337 (mmtp) REVERT: R 40 MET cc_start: 0.7961 (mtm) cc_final: 0.7662 (mtt) REVERT: R 64 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8276 (pp) REVERT: R 224 GLN cc_start: 0.7376 (mt0) cc_final: 0.7164 (tm-30) outliers start: 23 outliers final: 15 residues processed: 173 average time/residue: 0.2764 time to fit residues: 61.6473 Evaluate side-chains 163 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 144 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 226 GLU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.6980 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN B 340 ASN ** N 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7960 Z= 0.142 Angle : 0.503 8.677 10826 Z= 0.270 Chirality : 0.042 0.133 1255 Planarity : 0.003 0.049 1367 Dihedral : 5.909 86.751 1102 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 2.51 % Allowed : 20.18 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.07 (0.24), residues: 999 helix: -1.63 (0.26), residues: 357 sheet: -1.66 (0.33), residues: 225 loop : -2.50 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE R 289 TYR 0.012 0.001 TYR B 85 ARG 0.003 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 163 time to evaluate : 0.875 Fit side-chains revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7963 (m-30) cc_final: 0.7749 (m-30) REVERT: A 371 ASN cc_start: 0.8150 (m110) cc_final: 0.7949 (m110) REVERT: B 105 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8887 (t80) REVERT: N 87 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8249 (mmtp) REVERT: R 40 MET cc_start: 0.8006 (mtm) cc_final: 0.7730 (mtt) REVERT: R 64 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8085 (pp) outliers start: 20 outliers final: 13 residues processed: 174 average time/residue: 0.2329 time to fit residues: 52.4054 Evaluate side-chains 166 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 151 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 8.9990 chunk 47 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 0.0050 chunk 96 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 26 optimal weight: 0.4980 chunk 80 optimal weight: 0.5980 chunk 54 optimal weight: 9.9990 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7960 Z= 0.125 Angle : 0.469 6.425 10826 Z= 0.252 Chirality : 0.041 0.133 1255 Planarity : 0.003 0.048 1367 Dihedral : 5.380 89.725 1102 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.01 % Allowed : 21.55 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.54 (0.25), residues: 999 helix: -1.03 (0.27), residues: 364 sheet: -1.61 (0.33), residues: 212 loop : -2.21 (0.27), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 99 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE N 68 TYR 0.010 0.001 TYR B 59 ARG 0.002 0.000 ARG B 68 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 161 time to evaluate : 0.793 Fit side-chains REVERT: A 343 ASP cc_start: 0.7991 (m-30) cc_final: 0.7721 (m-30) REVERT: N 38 ARG cc_start: 0.8691 (ptt-90) cc_final: 0.8445 (ptt-90) REVERT: N 87 LYS cc_start: 0.8632 (ttmt) cc_final: 0.8184 (mmtp) REVERT: R 40 MET cc_start: 0.8131 (mtm) cc_final: 0.7922 (mtt) REVERT: R 64 LEU cc_start: 0.8222 (OUTLIER) cc_final: 0.7969 (pp) outliers start: 24 outliers final: 15 residues processed: 177 average time/residue: 0.2366 time to fit residues: 54.4231 Evaluate side-chains 168 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 152 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 45 LEU Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 0.8980 chunk 71 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 86 optimal weight: 0.2980 chunk 24 optimal weight: 0.0040 chunk 32 optimal weight: 3.9990 chunk 87 optimal weight: 7.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS N 39 GLN R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7960 Z= 0.127 Angle : 0.466 8.122 10826 Z= 0.246 Chirality : 0.041 0.132 1255 Planarity : 0.003 0.047 1367 Dihedral : 5.193 88.350 1102 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.76 % Allowed : 21.93 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.25), residues: 999 helix: -0.53 (0.29), residues: 354 sheet: -1.43 (0.34), residues: 212 loop : -2.09 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE N 68 TYR 0.010 0.001 TYR B 59 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 161 time to evaluate : 0.898 Fit side-chains REVERT: A 220 HIS cc_start: 0.7019 (OUTLIER) cc_final: 0.6792 (t-170) REVERT: B 234 PHE cc_start: 0.8781 (OUTLIER) cc_final: 0.7799 (t80) REVERT: N 38 ARG cc_start: 0.8613 (ptt-90) cc_final: 0.8372 (ptt-90) REVERT: N 87 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8181 (mmtp) REVERT: R 64 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.7983 (pp) outliers start: 30 outliers final: 20 residues processed: 179 average time/residue: 0.2168 time to fit residues: 51.0824 Evaluate side-chains 174 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 151 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 197 GLN Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 1.9990 chunk 56 optimal weight: 0.4980 chunk 23 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 93 optimal weight: 0.0170 chunk 10 optimal weight: 1.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS N 39 GLN R 65 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7960 Z= 0.133 Angle : 0.474 7.699 10826 Z= 0.250 Chirality : 0.041 0.134 1255 Planarity : 0.003 0.047 1367 Dihedral : 5.143 88.363 1102 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 4.01 % Allowed : 22.93 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.26), residues: 999 helix: -0.33 (0.29), residues: 354 sheet: -1.32 (0.34), residues: 212 loop : -2.00 (0.26), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 313 HIS 0.004 0.001 HIS A 357 PHE 0.011 0.001 PHE N 68 TYR 0.007 0.001 TYR R 174 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 0.955 Fit side-chains REVERT: A 220 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.6724 (t-170) REVERT: B 75 GLN cc_start: 0.8807 (mm-40) cc_final: 0.8441 (tp40) REVERT: B 234 PHE cc_start: 0.8775 (OUTLIER) cc_final: 0.7815 (t80) REVERT: N 87 LYS cc_start: 0.8640 (ttmt) cc_final: 0.8164 (mmtp) REVERT: R 64 LEU cc_start: 0.8296 (OUTLIER) cc_final: 0.8022 (pp) REVERT: R 304 ARG cc_start: 0.7625 (mtm180) cc_final: 0.7346 (mtm180) outliers start: 32 outliers final: 19 residues processed: 179 average time/residue: 0.2172 time to fit residues: 51.6030 Evaluate side-chains 178 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 0.0980 chunk 58 optimal weight: 0.0170 chunk 44 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 57 optimal weight: 0.0000 overall best weight: 0.6224 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS B 239 ASN N 39 GLN R 65 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7960 Z= 0.129 Angle : 0.472 6.740 10826 Z= 0.251 Chirality : 0.041 0.131 1255 Planarity : 0.003 0.047 1367 Dihedral : 5.086 88.697 1102 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.76 % Allowed : 22.81 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.26), residues: 999 helix: -0.12 (0.30), residues: 354 sheet: -1.29 (0.33), residues: 217 loop : -1.85 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 313 HIS 0.004 0.000 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.008 0.001 TYR R 174 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 220 HIS cc_start: 0.6968 (OUTLIER) cc_final: 0.6649 (t-170) REVERT: A 344 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8567 (mm-30) REVERT: B 75 GLN cc_start: 0.8799 (mm-40) cc_final: 0.8432 (tp40) REVERT: B 234 PHE cc_start: 0.8760 (OUTLIER) cc_final: 0.7811 (t80) REVERT: N 60 TYR cc_start: 0.9025 (m-80) cc_final: 0.8494 (m-80) REVERT: N 87 LYS cc_start: 0.8638 (ttmt) cc_final: 0.8164 (mmtp) REVERT: R 40 MET cc_start: 0.7840 (mtt) cc_final: 0.7512 (mtm) REVERT: R 64 LEU cc_start: 0.8266 (OUTLIER) cc_final: 0.7996 (pp) REVERT: R 304 ARG cc_start: 0.7598 (mtm180) cc_final: 0.7323 (mtm180) outliers start: 30 outliers final: 22 residues processed: 180 average time/residue: 0.2104 time to fit residues: 49.9744 Evaluate side-chains 185 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 160 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 197 GLN Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 65 optimal weight: 5.9990 chunk 47 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 92 optimal weight: 6.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN N 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7960 Z= 0.158 Angle : 0.473 6.480 10826 Z= 0.251 Chirality : 0.041 0.135 1255 Planarity : 0.003 0.047 1367 Dihedral : 5.135 89.314 1102 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.88 % Allowed : 22.68 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.26), residues: 999 helix: -0.03 (0.30), residues: 353 sheet: -1.08 (0.34), residues: 210 loop : -1.81 (0.27), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.009 0.001 PHE N 68 TYR 0.008 0.001 TYR R 174 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 158 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7216 (mtm-85) cc_final: 0.6772 (mtm-85) REVERT: A 220 HIS cc_start: 0.6725 (OUTLIER) cc_final: 0.6436 (t-90) REVERT: B 234 PHE cc_start: 0.8791 (OUTLIER) cc_final: 0.7814 (t80) REVERT: N 60 TYR cc_start: 0.9059 (m-80) cc_final: 0.8574 (m-80) REVERT: N 70 ILE cc_start: 0.8887 (tt) cc_final: 0.8605 (pt) REVERT: N 87 LYS cc_start: 0.8651 (ttmt) cc_final: 0.8213 (mmtp) REVERT: R 40 MET cc_start: 0.7965 (mtt) cc_final: 0.7685 (mtm) REVERT: R 64 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8009 (pp) REVERT: R 304 ARG cc_start: 0.7603 (mtm180) cc_final: 0.7327 (mtm180) outliers start: 31 outliers final: 25 residues processed: 179 average time/residue: 0.2168 time to fit residues: 51.1522 Evaluate side-chains 182 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 154 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 197 GLN Chi-restraints excluded: chain R residue 215 MET Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 6.9990 chunk 54 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.4980 chunk 84 optimal weight: 0.9990 chunk 89 optimal weight: 0.4980 chunk 58 optimal weight: 3.9990 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 8.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS R 322 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7960 Z= 0.198 Angle : 0.495 6.268 10826 Z= 0.264 Chirality : 0.042 0.139 1255 Planarity : 0.003 0.048 1367 Dihedral : 5.204 83.449 1102 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 4.14 % Allowed : 22.43 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.45 (0.26), residues: 999 helix: 0.11 (0.30), residues: 350 sheet: -1.01 (0.34), residues: 209 loop : -1.78 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.006 0.001 HIS A 357 PHE 0.011 0.001 PHE N 68 TYR 0.010 0.001 TYR B 85 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 158 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.8039 (m-30) cc_final: 0.7713 (m-30) REVERT: A 344 GLU cc_start: 0.8859 (mm-30) cc_final: 0.8620 (mm-30) REVERT: B 75 GLN cc_start: 0.8924 (tp40) cc_final: 0.8645 (tp40) REVERT: B 105 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.8712 (t80) REVERT: B 118 ASP cc_start: 0.8338 (p0) cc_final: 0.8023 (p0) REVERT: B 234 PHE cc_start: 0.8855 (OUTLIER) cc_final: 0.8047 (t80) REVERT: N 60 TYR cc_start: 0.9061 (m-80) cc_final: 0.8572 (m-80) REVERT: N 70 ILE cc_start: 0.8928 (tt) cc_final: 0.8619 (pt) REVERT: N 87 LYS cc_start: 0.8672 (ttmt) cc_final: 0.8209 (mmtp) REVERT: R 40 MET cc_start: 0.7913 (mtt) cc_final: 0.7681 (mtm) REVERT: R 64 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8078 (pp) outliers start: 33 outliers final: 27 residues processed: 180 average time/residue: 0.2140 time to fit residues: 51.1019 Evaluate side-chains 183 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 197 GLN Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 24 optimal weight: 0.2980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7960 Z= 0.167 Angle : 0.493 7.406 10826 Z= 0.262 Chirality : 0.042 0.139 1255 Planarity : 0.003 0.048 1367 Dihedral : 5.094 81.754 1102 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.90 % Favored : 95.10 % Rotamer: Outliers : 3.76 % Allowed : 22.81 % Favored : 73.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.26), residues: 999 helix: 0.18 (0.30), residues: 350 sheet: -0.98 (0.34), residues: 214 loop : -1.68 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 109 HIS 0.005 0.001 HIS A 357 PHE 0.010 0.001 PHE N 68 TYR 0.009 0.001 TYR B 59 ARG 0.006 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1998 Ramachandran restraints generated. 999 Oldfield, 0 Emsley, 999 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ARG cc_start: 0.7260 (mtm-85) cc_final: 0.6889 (mtm-85) REVERT: A 344 GLU cc_start: 0.8855 (mm-30) cc_final: 0.8617 (mm-30) REVERT: B 61 MET cc_start: 0.8299 (ppp) cc_final: 0.7950 (ptm) REVERT: B 105 TYR cc_start: 0.9133 (OUTLIER) cc_final: 0.8559 (t80) REVERT: B 118 ASP cc_start: 0.8332 (p0) cc_final: 0.8026 (p0) REVERT: B 234 PHE cc_start: 0.8822 (OUTLIER) cc_final: 0.7909 (t80) REVERT: N 60 TYR cc_start: 0.9055 (m-80) cc_final: 0.8550 (m-80) REVERT: N 70 ILE cc_start: 0.8905 (tt) cc_final: 0.8602 (pt) REVERT: N 87 LYS cc_start: 0.8724 (ttmt) cc_final: 0.8213 (mmtp) REVERT: R 40 MET cc_start: 0.7801 (mtt) cc_final: 0.7543 (mtm) REVERT: R 64 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8050 (pp) outliers start: 30 outliers final: 27 residues processed: 177 average time/residue: 0.2138 time to fit residues: 50.0254 Evaluate side-chains 185 residues out of total 875 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 63 TRP Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 183 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 255 LEU Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 31 ASN Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 84 LEU Chi-restraints excluded: chain R residue 125 VAL Chi-restraints excluded: chain R residue 144 LEU Chi-restraints excluded: chain R residue 183 ASN Chi-restraints excluded: chain R residue 190 CYS Chi-restraints excluded: chain R residue 197 GLN Chi-restraints excluded: chain R residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 33 optimal weight: 8.9990 chunk 81 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110269 restraints weight = 10492.607| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 2.20 r_work: 0.3019 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7960 Z= 0.139 Angle : 0.475 7.315 10826 Z= 0.252 Chirality : 0.041 0.133 1255 Planarity : 0.003 0.048 1367 Dihedral : 4.933 80.379 1102 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 4.01 % Allowed : 23.06 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.27), residues: 999 helix: 0.34 (0.30), residues: 346 sheet: -0.87 (0.35), residues: 213 loop : -1.62 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 234 HIS 0.007 0.001 HIS A 220 PHE 0.009 0.001 PHE A 212 TYR 0.008 0.001 TYR R 174 ARG 0.006 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2104.27 seconds wall clock time: 38 minutes 49.10 seconds (2329.10 seconds total)