Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 03:16:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/10_2023/8f2a_28810_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/10_2023/8f2a_28810.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/10_2023/8f2a_28810.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/10_2023/8f2a_28810.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/10_2023/8f2a_28810_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f2a_28810/10_2023/8f2a_28810_updated.pdb" } resolution = 2.2 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= -0.002 sd= 0.100 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 75 5.16 5 C 6392 2.51 5 N 1734 2.21 5 O 1843 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E GLU 74": "OE1" <-> "OE2" Residue "E ARG 98": "NH1" <-> "NH2" Residue "P ARG 11": "NH1" <-> "NH2" Residue "P PHE 23": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 101": "OD1" <-> "OD2" Residue "R ASP 103": "OD1" <-> "OD2" Residue "R ARG 126": "NH1" <-> "NH2" Residue "R TYR 131": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 255": "OE1" <-> "OE2" Residue "R ARG 258": "NH1" <-> "NH2" Residue "R GLU 294": "OE1" <-> "OE2" Residue "R ARG 321": "NH1" <-> "NH2" Residue "R GLU 329": "OE1" <-> "OE2" Residue "R GLU 334": "OE1" <-> "OE2" Residue "R ARG 362": "NH1" <-> "NH2" Residue "R TYR 391": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 397": "OE1" <-> "OE2" Residue "R ARG 404": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ARG 231": "NH1" <-> "NH2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ASP 323": "OD1" <-> "OD2" Residue "A GLU 327": "OE1" <-> "OE2" Residue "A ASP 331": "OD1" <-> "OD2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "B GLU 12": "OE1" <-> "OE2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B PHE 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 214": "NH1" <-> "NH2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 304": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 62": "NH1" <-> "NH2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 10044 Number of models: 1 Model: "" Number of chains: 9 Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 810 Classifications: {'peptide': 117} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 109} Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 98 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 59 Chain: "P" Number of atoms: 280 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 280 Unusual residues: {'NH2': 1} Classifications: {'peptide': 37, 'undetermined': 1} Link IDs: {'NH2_CTERM': 1, 'PTRANS': 3, 'TRANS': 33} Chain: "R" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2996 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 16, 'TRANS': 352} Unresolved non-hydrogen bonds: 72 Unresolved non-hydrogen angles: 87 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 1, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1899 Classifications: {'peptide': 231} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 2606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2606 Classifications: {'peptide': 339} Link IDs: {'PTRANS': 5, 'TRANS': 333} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 973 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 973 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 5.49, per 1000 atoms: 0.55 Number of scatterers: 10044 At special positions: 0 Unit cell: (93.4375, 168.188, 92.625, 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 75 16.00 O 1843 8.00 N 1734 7.00 C 6392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS E 28 " - pdb=" SG CYS E 82 " distance=2.03 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 72 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS P 2 " - pdb=" SG CYS P 7 " distance=2.03 Simple disulfide: pdb=" SG CYS R 55 " - pdb=" SG CYS R 81 " distance=2.03 Simple disulfide: pdb=" SG CYS R 72 " - pdb=" SG CYS R 112 " distance=2.03 Simple disulfide: pdb=" SG CYS R 95 " - pdb=" SG CYS R 134 " distance=2.03 Simple disulfide: pdb=" SG CYS R 219 " - pdb=" SG CYS R 289 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.04 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 Links applied NAG-ASN " NAG E 201 " - " ASN E 29 " " NAG E 202 " - " ASN E 71 " " NAG R 501 " - " ASN R 73 " " NAG R 502 " - " ASN R 130 " Time building additional restraints: 4.03 Conformation dependent library (CDL) restraints added in 1.4 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2400 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 11 sheets defined 38.4% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'E' and resid 30 through 47 removed outlier: 3.619A pdb=" N LEU E 34 " --> pdb=" O GLU E 30 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLU E 35 " --> pdb=" O THR E 31 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG E 36 " --> pdb=" O GLY E 32 " (cutoff:3.500A) Proline residue: E 38 - end of helix removed outlier: 3.555A pdb=" N GLY E 41 " --> pdb=" O LEU E 37 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 63 No H-bonds generated for 'chain 'E' and resid 61 through 63' Processing helix chain 'E' and resid 65 through 75 removed outlier: 3.848A pdb=" N THR E 70 " --> pdb=" O TYR E 66 " (cutoff:3.500A) Processing helix chain 'E' and resid 89 through 100 removed outlier: 3.605A pdb=" N GLN E 99 " --> pdb=" O GLY E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 119 No H-bonds generated for 'chain 'E' and resid 116 through 119' Processing helix chain 'E' and resid 121 through 140 Proline residue: E 126 - end of helix removed outlier: 3.613A pdb=" N VAL E 138 " --> pdb=" O ALA E 134 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 15 removed outlier: 5.044A pdb=" N THR P 9 " --> pdb=" O THR P 6 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN P 14 " --> pdb=" O ARG P 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 61 removed outlier: 3.589A pdb=" N GLN R 60 " --> pdb=" O TYR R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 132 through 135 No H-bonds generated for 'chain 'R' and resid 132 through 135' Processing helix chain 'R' and resid 138 through 172 removed outlier: 3.612A pdb=" N VAL R 147 " --> pdb=" O LYS R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 179 through 203 removed outlier: 3.536A pdb=" N ASN R 186 " --> pdb=" O THR R 182 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 214 removed outlier: 3.580A pdb=" N ARG R 213 " --> pdb=" O GLY R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 248 removed outlier: 3.505A pdb=" N MET R 237 " --> pdb=" O ASN R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 266 Processing helix chain 'R' and resid 269 through 283 Proline residue: R 273 - end of helix removed outlier: 3.637A pdb=" N ILE R 276 " --> pdb=" O PRO R 273 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N HIS R 277 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ILE R 279 " --> pdb=" O ILE R 276 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ARG R 281 " --> pdb=" O ALA R 278 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA R 282 " --> pdb=" O ILE R 279 " (cutoff:3.500A) Processing helix chain 'R' and resid 288 through 290 No H-bonds generated for 'chain 'R' and resid 288 through 290' Processing helix chain 'R' and resid 296 through 329 removed outlier: 3.507A pdb=" N TYR R 299 " --> pdb=" O HIS R 296 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N HIS R 302 " --> pdb=" O TYR R 299 " (cutoff:3.500A) removed outlier: 4.989A pdb=" N GLY R 303 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Proline residue: R 304 - end of helix removed outlier: 3.902A pdb=" N VAL R 310 " --> pdb=" O ALA R 307 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL R 311 " --> pdb=" O ALA R 308 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU R 317 " --> pdb=" O PHE R 314 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG R 321 " --> pdb=" O ASN R 318 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL R 324 " --> pdb=" O ARG R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 334 through 352 Proline residue: R 350 - end of helix Processing helix chain 'R' and resid 354 through 358 removed outlier: 3.923A pdb=" N VAL R 358 " --> pdb=" O GLN R 355 " (cutoff:3.500A) Processing helix chain 'R' and resid 366 through 381 removed outlier: 3.632A pdb=" N SER R 378 " --> pdb=" O TYR R 374 " (cutoff:3.500A) Processing helix chain 'R' and resid 383 through 391 Processing helix chain 'R' and resid 396 through 404 Processing helix chain 'A' and resid 12 through 39 Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 280 through 282 No H-bonds generated for 'chain 'A' and resid 280 through 282' Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' 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 351 removed outlier: 3.833A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA A 351 " --> pdb=" O ARG A 347 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.793A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 11 through 21 Processing helix chain 'G' and resid 30 through 43 removed outlier: 3.553A pdb=" N LEU G 37 " --> pdb=" O ALA G 33 " (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 sheet with id= A, first strand: chain 'R' and resid 89 through 94 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.211A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLY A 47 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.918A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.899A 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: 6.824A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.673A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.859A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.579A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.421A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.537A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.089A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1134 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: 2.98 Time building geometry restraints manager: 4.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3262 1.34 - 1.46: 2532 1.46 - 1.58: 4382 1.58 - 1.70: 0 1.70 - 1.82: 106 Bond restraints: 10282 Sorted by residual: bond pdb=" N VAL R 171 " pdb=" CA VAL R 171 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.98e+00 bond pdb=" N HIS B 311 " pdb=" CA HIS B 311 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.28e-02 6.10e+03 7.46e+00 bond pdb=" N ILE B 338 " pdb=" CA ILE B 338 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.27e-02 6.20e+03 7.18e+00 bond pdb=" N LYS A 24 " pdb=" CA LYS A 24 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.23e-02 6.61e+03 6.66e+00 bond pdb=" N LEU A 30 " pdb=" CA LEU A 30 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.63e+00 ... (remaining 10277 not shown) Histogram of bond angle deviations from ideal: 100.36 - 107.12: 290 107.12 - 113.88: 5731 113.88 - 120.64: 4248 120.64 - 127.40: 3568 127.40 - 134.16: 128 Bond angle restraints: 13965 Sorted by residual: angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 111.81 107.88 3.93 8.60e-01 1.35e+00 2.08e+01 angle pdb=" N HIS B 311 " pdb=" CA HIS B 311 " pdb=" C HIS B 311 " ideal model delta sigma weight residual 110.10 116.66 -6.56 1.49e+00 4.50e-01 1.94e+01 angle pdb=" N ARG R 174 " pdb=" CA ARG R 174 " pdb=" C ARG R 174 " ideal model delta sigma weight residual 112.54 107.20 5.34 1.22e+00 6.72e-01 1.91e+01 angle pdb=" CA GLY R 177 " pdb=" C GLY R 177 " pdb=" O GLY R 177 " ideal model delta sigma weight residual 121.41 118.14 3.27 8.80e-01 1.29e+00 1.38e+01 angle pdb=" N LEU R 176 " pdb=" CA LEU R 176 " pdb=" C LEU R 176 " ideal model delta sigma weight residual 112.54 108.15 4.39 1.22e+00 6.72e-01 1.29e+01 ... (remaining 13960 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 5496 17.59 - 35.18: 434 35.18 - 52.77: 86 52.77 - 70.36: 22 70.36 - 87.96: 10 Dihedral angle restraints: 6048 sinusoidal: 2330 harmonic: 3718 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 161.90 -68.90 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CB CYS E 57 " pdb=" SG CYS E 57 " pdb=" SG CYS E 104 " pdb=" CB CYS E 104 " ideal model delta sinusoidal sigma weight residual -86.00 -27.97 -58.03 1 1.00e+01 1.00e-02 4.52e+01 dihedral pdb=" CB CYS R 95 " pdb=" SG CYS R 95 " pdb=" SG CYS R 134 " pdb=" CB CYS R 134 " ideal model delta sinusoidal sigma weight residual 93.00 130.91 -37.91 1 1.00e+01 1.00e-02 2.03e+01 ... (remaining 6045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 1348 0.061 - 0.122: 185 0.122 - 0.183: 20 0.183 - 0.243: 4 0.243 - 0.304: 3 Chirality restraints: 1560 Sorted by residual: chirality pdb=" CA HIS B 311 " pdb=" N HIS B 311 " pdb=" C HIS B 311 " pdb=" CB HIS B 311 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.32e+00 chirality pdb=" CA LEU B 308 " pdb=" N LEU B 308 " pdb=" C LEU B 308 " pdb=" CB LEU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.60e+00 chirality pdb=" CA LEU B 336 " pdb=" N LEU B 336 " pdb=" C LEU B 336 " pdb=" CB LEU B 336 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 1557 not shown) Planarity restraints: 1788 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 312 " 0.013 2.00e-02 2.50e+03 2.68e-02 7.21e+00 pdb=" C ASP B 312 " -0.046 2.00e-02 2.50e+03 pdb=" O ASP B 312 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN B 313 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE R 269 " 0.028 5.00e-02 4.00e+02 4.30e-02 2.96e+00 pdb=" N PRO R 270 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO R 270 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 270 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.027 5.00e-02 4.00e+02 4.08e-02 2.66e+00 pdb=" N PRO B 236 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.023 5.00e-02 4.00e+02 ... (remaining 1785 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 487 2.73 - 3.27: 10264 3.27 - 3.82: 16943 3.82 - 4.36: 22129 4.36 - 4.90: 35922 Nonbonded interactions: 85745 Sorted by model distance: nonbonded pdb=" OE1 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.188 2.440 nonbonded pdb=" OD1 ASN R 130 " pdb=" OG1 THR R 132 " model vdw 2.252 2.440 nonbonded pdb=" O SER N 112 " pdb=" NH2 ARG N 118 " model vdw 2.253 2.520 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.289 2.440 nonbonded pdb=" NH2 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.292 2.520 ... (remaining 85740 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=0.00 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: 1.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 7.350 Check model and map are aligned: 0.150 Set scattering table: 0.090 Process input model: 29.570 Find NCS groups from input model: 0.280 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: 0.000 Load rotamer database and sin/cos tables:11.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 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 0.035 10282 Z= 0.229 Angle : 0.602 7.805 13965 Z= 0.383 Chirality : 0.046 0.304 1560 Planarity : 0.003 0.043 1784 Dihedral : 13.840 87.956 3618 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.76 % Allowed : 6.84 % Favored : 92.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % 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: -2.70 (0.20), residues: 1258 helix: -2.68 (0.16), residues: 497 sheet: -0.61 (0.31), residues: 237 loop : -1.20 (0.24), residues: 524 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 170 time to evaluate : 1.119 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 177 average time/residue: 1.3196 time to fit residues: 249.3590 Evaluate side-chains 147 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.935 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1128 time to fit residues: 1.5201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 9.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 5.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 97 HIS P 3 ASN P 18 HIS P 31 ASN R 121 HIS R 179 GLN R 186 ASN R 227 GLN R 383 GLN R 395 ASN ** R 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 294 GLN B 6 GLN B 17 GLN B 88 ASN B 175 GLN B 268 ASN B 293 ASN N 82 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10282 Z= 0.276 Angle : 0.612 7.699 13965 Z= 0.332 Chirality : 0.045 0.177 1560 Planarity : 0.005 0.050 1784 Dihedral : 4.902 26.897 1385 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.09 % Allowed : 12.35 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.21), residues: 1258 helix: -0.37 (0.21), residues: 498 sheet: -0.26 (0.31), residues: 234 loop : -0.78 (0.25), residues: 526 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 156 time to evaluate : 1.185 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 8 residues processed: 167 average time/residue: 1.3633 time to fit residues: 243.5289 Evaluate side-chains 151 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 143 time to evaluate : 1.985 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.2503 time to fit residues: 2.7271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 5.9990 chunk 120 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 110 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 31 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 383 GLN ** R 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 54 ASN B 268 ASN N 82 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10282 Z= 0.243 Angle : 0.573 7.456 13965 Z= 0.309 Chirality : 0.044 0.150 1560 Planarity : 0.004 0.052 1784 Dihedral : 4.813 21.294 1385 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.47 % Allowed : 14.43 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.22), residues: 1258 helix: 0.45 (0.23), residues: 500 sheet: -0.12 (0.31), residues: 231 loop : -0.70 (0.24), residues: 527 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 152 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 10 residues processed: 167 average time/residue: 1.4017 time to fit residues: 249.7114 Evaluate side-chains 157 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 147 time to evaluate : 1.162 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 8 residues processed: 3 average time/residue: 0.6135 time to fit residues: 3.6261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 268 ASN N 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10282 Z= 0.266 Angle : 0.579 7.540 13965 Z= 0.311 Chirality : 0.044 0.153 1560 Planarity : 0.004 0.052 1784 Dihedral : 4.875 22.169 1385 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.94 % Allowed : 14.81 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.22), residues: 1258 helix: 0.67 (0.23), residues: 505 sheet: -0.06 (0.31), residues: 234 loop : -0.56 (0.25), residues: 519 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 153 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 173 average time/residue: 1.2898 time to fit residues: 239.0115 Evaluate side-chains 163 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 1.171 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 9 residues processed: 7 average time/residue: 0.3793 time to fit residues: 4.9408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 1.9990 chunk 1 optimal weight: 6.9990 chunk 88 optimal weight: 4.9990 chunk 49 optimal weight: 0.0020 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 40.0000 chunk 60 optimal weight: 0.5980 chunk 106 optimal weight: 3.9990 chunk 30 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN P 22 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10282 Z= 0.204 Angle : 0.540 7.217 13965 Z= 0.288 Chirality : 0.043 0.177 1560 Planarity : 0.004 0.052 1784 Dihedral : 4.703 23.921 1385 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 2.66 % Allowed : 15.19 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.23), residues: 1258 helix: 0.94 (0.23), residues: 506 sheet: 0.08 (0.32), residues: 229 loop : -0.53 (0.25), residues: 523 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 13 residues processed: 164 average time/residue: 1.4102 time to fit residues: 246.7321 Evaluate side-chains 154 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.193 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 5 average time/residue: 0.4737 time to fit residues: 4.3687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.0050 chunk 23 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.3980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 387 HIS B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10282 Z= 0.144 Angle : 0.494 8.457 13965 Z= 0.262 Chirality : 0.041 0.168 1560 Planarity : 0.004 0.053 1784 Dihedral : 4.379 20.080 1385 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.18 % Allowed : 16.05 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.23), residues: 1258 helix: 1.28 (0.24), residues: 507 sheet: 0.15 (0.32), residues: 226 loop : -0.51 (0.25), residues: 525 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.107 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 12 residues processed: 160 average time/residue: 1.4039 time to fit residues: 239.9984 Evaluate side-chains 151 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.098 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 3 average time/residue: 0.6080 time to fit residues: 3.5819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN N 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10282 Z= 0.176 Angle : 0.526 7.592 13965 Z= 0.278 Chirality : 0.042 0.151 1560 Planarity : 0.004 0.053 1784 Dihedral : 4.495 29.035 1385 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.18 % Allowed : 16.14 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1258 helix: 1.35 (0.24), residues: 507 sheet: 0.11 (0.32), residues: 227 loop : -0.48 (0.25), residues: 524 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 138 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 14 residues processed: 154 average time/residue: 1.3977 time to fit residues: 229.8777 Evaluate side-chains 149 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 135 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 11 residues processed: 4 average time/residue: 0.4935 time to fit residues: 3.7525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 7.9990 chunk 35 optimal weight: 10.0000 chunk 23 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 107 optimal weight: 8.9990 chunk 113 optimal weight: 0.8980 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 10282 Z= 0.387 Angle : 0.661 8.239 13965 Z= 0.354 Chirality : 0.048 0.159 1560 Planarity : 0.005 0.052 1784 Dihedral : 5.086 26.362 1385 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.99 % Allowed : 16.33 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.23), residues: 1258 helix: 0.87 (0.23), residues: 506 sheet: 0.00 (0.32), residues: 235 loop : -0.52 (0.25), residues: 517 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 12 residues processed: 160 average time/residue: 1.3375 time to fit residues: 228.9547 Evaluate side-chains 154 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 142 time to evaluate : 1.097 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 2 average time/residue: 0.8738 time to fit residues: 3.4446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 0.1980 chunk 113 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 99 optimal weight: 0.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10282 Z= 0.165 Angle : 0.527 8.408 13965 Z= 0.279 Chirality : 0.042 0.163 1560 Planarity : 0.004 0.052 1784 Dihedral : 4.605 24.193 1385 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.71 % Allowed : 17.28 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1258 helix: 1.22 (0.24), residues: 507 sheet: 0.10 (0.32), residues: 230 loop : -0.49 (0.25), residues: 521 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 145 time to evaluate : 1.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 158 average time/residue: 1.3786 time to fit residues: 232.5824 Evaluate side-chains 151 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.964 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1628 time to fit residues: 2.3758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 81 optimal weight: 0.0060 chunk 122 optimal weight: 1.9990 chunk 112 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10282 Z= 0.150 Angle : 0.520 8.843 13965 Z= 0.272 Chirality : 0.041 0.205 1560 Planarity : 0.004 0.054 1784 Dihedral : 4.392 23.097 1385 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.23 % Allowed : 17.85 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.23), residues: 1258 helix: 1.41 (0.24), residues: 507 sheet: 0.17 (0.32), residues: 226 loop : -0.44 (0.25), residues: 525 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 1.126 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 149 average time/residue: 1.6361 time to fit residues: 261.6669 Evaluate side-chains 147 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.135 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 10 residues processed: 1 average time/residue: 0.3164 time to fit residues: 1.9763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 97 optimal weight: 0.0020 chunk 40 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.1192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: P 3 ASN ** R 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 405 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.196624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.131791 restraints weight = 10656.280| |-----------------------------------------------------------------------------| r_work (start): 0.3604 rms_B_bonded: 1.75 r_work: 0.3488 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10282 Z= 0.184 Angle : 0.534 8.445 13965 Z= 0.283 Chirality : 0.042 0.193 1560 Planarity : 0.004 0.054 1784 Dihedral : 4.517 22.417 1385 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.42 % Allowed : 17.57 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.23), residues: 1258 helix: 1.41 (0.24), residues: 506 sheet: 0.12 (0.32), residues: 231 loop : -0.40 (0.25), residues: 521 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4693.43 seconds wall clock time: 83 minutes 37.46 seconds (5017.46 seconds total)