Starting phenix.real_space_refine on Thu Jan 18 05:30:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx4_30491/01_2024/7cx4_30491_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx4_30491/01_2024/7cx4_30491.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx4_30491/01_2024/7cx4_30491.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx4_30491/01_2024/7cx4_30491.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx4_30491/01_2024/7cx4_30491_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx4_30491/01_2024/7cx4_30491_updated.pdb" } resolution = 2.9 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= 0.011 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 53 5.16 5 C 5026 2.51 5 N 1372 2.21 5 O 1475 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R ASP 78": "OD1" <-> "OD2" Residue "R ARG 107": "NH1" <-> "NH2" Residue "R PHE 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 174": "OD1" <-> "OD2" Residue "R TYR 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R GLU 259": "OE1" <-> "OE2" Residue "R ARG 302": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ASP 215": "OD1" <-> "OD2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A TYR 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A PHE 312": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 330": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 360": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ASP 381": "OD1" <-> "OD2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "B ARG 42": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ASP 118": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ASP 254": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ASP 267": "OD1" <-> "OD2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G ASP 26": "OD1" <-> "OD2" Residue "G GLU 42": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "N ARG 105": "NH1" <-> "NH2" Residue "N ASP 109": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7926 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2016 Classifications: {'peptide': 266} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 254} Chain breaks: 2 Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 7, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 53 Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1870 Classifications: {'peptide': 228} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 6, 'TRANS': 221} Chain breaks: 2 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 2598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2598 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "G" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 438 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 971 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'GM9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.74, per 1000 atoms: 0.60 Number of scatterers: 7926 At special positions: 0 Unit cell: (76.05, 110.526, 125.736, 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 53 16.00 O 1475 8.00 N 1372 7.00 C 5026 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 187 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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 1.4 seconds 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1922 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 26 helices and 11 sheets defined 35.8% alpha, 20.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.66 Creating SS restraints... Processing helix chain 'R' and resid 26 through 44 removed outlier: 3.512A pdb=" N MET R 31 " --> pdb=" O ILE R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 93 Proline residue: R 87 - end of helix removed outlier: 3.685A pdb=" N SER R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 139 Processing helix chain 'R' and resid 141 through 147 removed outlier: 3.590A pdb=" N ARG R 146 " --> pdb=" O TYR R 142 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG R 147 " --> pdb=" O PHE R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 169 removed outlier: 3.793A pdb=" N LEU R 154 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA R 155 " --> pdb=" O GLY R 152 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU R 157 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 158 - end of helix removed outlier: 3.736A pdb=" N TYR R 161 " --> pdb=" O PRO R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 227 Processing helix chain 'R' and resid 259 through 275 Processing helix chain 'R' and resid 278 through 283 Processing helix chain 'R' and resid 288 through 294 Processing helix chain 'R' and resid 297 through 316 removed outlier: 3.546A pdb=" N LEU R 301 " --> pdb=" O ASP R 297 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LEU R 304 " --> pdb=" O ALA R 300 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 320 through 329 Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.660A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 294 through 303 Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.920A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.577A pdb=" N ARG A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 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 6 through 22 removed outlier: 3.687A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 43 Processing helix chain 'G' and resid 45 through 47 No H-bonds generated for 'chain 'G' and resid 45 through 47' 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 178 through 180 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 363 removed outlier: 7.006A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.766A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.718A 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: 6.901A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.752A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.072A 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: 6.457A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.352A 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: 6.921A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.340A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.433A 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: 6.620A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.728A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.586A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.559A 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: 6.279A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 356 hydrogen bonds defined for protein. 1005 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: 2.27 Time building geometry restraints manager: 3.17 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: 2594 1.34 - 1.47: 1990 1.47 - 1.59: 3425 1.59 - 1.72: 0 1.72 - 1.84: 76 Bond restraints: 8085 Sorted by residual: bond pdb=" C25 GM9 R 401 " pdb=" O04 GM9 R 401 " ideal model delta sigma weight residual 1.246 1.355 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N01 GM9 R 401 " pdb=" S01 GM9 R 401 " ideal model delta sigma weight residual 1.640 1.723 -0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" C24 GM9 R 401 " pdb=" C25 GM9 R 401 " ideal model delta sigma weight residual 1.541 1.505 0.036 2.00e-02 2.50e+03 3.25e+00 bond pdb=" C ARG R 147 " pdb=" O ARG R 147 " ideal model delta sigma weight residual 1.237 1.218 0.019 1.17e-02 7.31e+03 2.51e+00 bond pdb=" C LEU R 157 " pdb=" O LEU R 157 " ideal model delta sigma weight residual 1.244 1.231 0.013 9.80e-03 1.04e+04 1.75e+00 ... (remaining 8080 not shown) Histogram of bond angle deviations from ideal: 99.68 - 106.56: 175 106.56 - 113.45: 4417 113.45 - 120.33: 3072 120.33 - 127.21: 3225 127.21 - 134.09: 79 Bond angle restraints: 10968 Sorted by residual: angle pdb=" N ARG R 147 " pdb=" CA ARG R 147 " pdb=" C ARG R 147 " ideal model delta sigma weight residual 111.28 119.77 -8.49 1.09e+00 8.42e-01 6.07e+01 angle pdb=" C GLY A 355 " pdb=" N ARG A 356 " pdb=" CA ARG A 356 " ideal model delta sigma weight residual 122.36 113.24 9.12 1.42e+00 4.96e-01 4.12e+01 angle pdb=" CA LEU R 157 " pdb=" C LEU R 157 " pdb=" N PRO R 158 " ideal model delta sigma weight residual 120.93 117.05 3.88 1.06e+00 8.90e-01 1.34e+01 angle pdb=" C LEU R 157 " pdb=" N PRO R 158 " pdb=" CA PRO R 158 " ideal model delta sigma weight residual 119.05 122.80 -3.75 1.11e+00 8.12e-01 1.14e+01 angle pdb=" N ARG R 146 " pdb=" CA ARG R 146 " pdb=" C ARG R 146 " ideal model delta sigma weight residual 112.68 116.98 -4.30 1.33e+00 5.65e-01 1.04e+01 ... (remaining 10963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4399 17.53 - 35.06: 345 35.06 - 52.59: 52 52.59 - 70.12: 10 70.12 - 87.65: 5 Dihedral angle restraints: 4811 sinusoidal: 1842 harmonic: 2969 Sorted by residual: dihedral pdb=" CB CYS R 109 " pdb=" SG CYS R 109 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual 93.00 5.35 87.65 1 1.00e+01 1.00e-02 9.21e+01 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 -86.00 -9.03 -76.97 1 1.00e+01 1.00e-02 7.44e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -150.13 -29.87 0 5.00e+00 4.00e-02 3.57e+01 ... (remaining 4808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1163 0.084 - 0.168: 83 0.168 - 0.252: 0 0.252 - 0.336: 0 0.336 - 0.420: 1 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CA ARG R 147 " pdb=" N ARG R 147 " pdb=" C ARG R 147 " pdb=" CB ARG R 147 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA TYR A 391 " pdb=" N TYR A 391 " pdb=" C TYR A 391 " pdb=" CB TYR A 391 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA ILE B 123 " pdb=" N ILE B 123 " pdb=" C ILE B 123 " pdb=" CB ILE B 123 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 1244 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 352 " -0.014 2.00e-02 2.50e+03 2.97e-02 8.82e+00 pdb=" C SER A 352 " 0.051 2.00e-02 2.50e+03 pdb=" O SER A 352 " -0.020 2.00e-02 2.50e+03 pdb=" N GLY A 353 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 318 " -0.011 2.00e-02 2.50e+03 2.20e-02 4.86e+00 pdb=" C LEU R 318 " 0.038 2.00e-02 2.50e+03 pdb=" O LEU R 318 " -0.014 2.00e-02 2.50e+03 pdb=" N ARG R 319 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.016 2.00e-02 2.50e+03 1.48e-02 4.39e+00 pdb=" CG TYR B 59 " 0.036 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.001 2.00e-02 2.50e+03 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.61: 72 2.61 - 3.18: 6629 3.18 - 3.75: 11980 3.75 - 4.33: 17136 4.33 - 4.90: 28987 Nonbonded interactions: 64804 Sorted by model distance: nonbonded pdb=" O ARG A 283 " pdb=" O GLY A 355 " model vdw 2.032 3.040 nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.106 2.440 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.129 2.440 nonbonded pdb=" OG SER A 251 " pdb=" O LYS A 293 " model vdw 2.130 2.440 nonbonded pdb=" O ALA A 351 " pdb=" OG SER A 352 " model vdw 2.169 2.440 ... (remaining 64799 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: 0.760 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: 1.930 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.890 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:12.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 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 0.109 8085 Z= 0.270 Angle : 0.643 9.118 10968 Z= 0.386 Chirality : 0.045 0.420 1247 Planarity : 0.004 0.040 1400 Dihedral : 12.918 81.309 2880 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: -1.78 (0.24), residues: 1002 helix: -0.41 (0.25), residues: 374 sheet: -1.00 (0.30), residues: 232 loop : -1.94 (0.28), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.010 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.036 0.001 TYR B 59 ARG 0.005 0.000 ARG G 13 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 179 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8275 (mt-10) cc_final: 0.7986 (tt0) REVERT: B 61 MET cc_start: 0.8513 (tmm) cc_final: 0.8190 (ptm) REVERT: B 246 ASP cc_start: 0.7973 (m-30) cc_final: 0.7598 (m-30) REVERT: N 3 GLN cc_start: 0.7641 (tp40) cc_final: 0.7041 (mt0) REVERT: N 38 ARG cc_start: 0.8908 (ptt180) cc_final: 0.8636 (ptp90) outliers start: 0 outliers final: 1 residues processed: 179 average time/residue: 1.2879 time to fit residues: 242.8389 Evaluate side-chains 138 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 41 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 25 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 35 GLN ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 292 ASN B 16 ASN N 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8085 Z= 0.250 Angle : 0.576 10.008 10968 Z= 0.298 Chirality : 0.043 0.163 1247 Planarity : 0.004 0.044 1400 Dihedral : 4.793 38.595 1121 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.99 % Allowed : 12.31 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.79 (0.25), residues: 1002 helix: 0.67 (0.27), residues: 380 sheet: -0.70 (0.31), residues: 231 loop : -1.54 (0.29), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.009 0.002 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.013 0.001 TYR R 144 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7831 (mtpp) cc_final: 0.7567 (mtmm) REVERT: A 314 GLU cc_start: 0.8258 (mt-10) cc_final: 0.7969 (tt0) REVERT: A 378 ASP cc_start: 0.7424 (m-30) cc_final: 0.7160 (m-30) REVERT: B 61 MET cc_start: 0.8524 (tmm) cc_final: 0.8017 (ptm) REVERT: B 134 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6932 (ptm-80) REVERT: B 246 ASP cc_start: 0.7936 (m-30) cc_final: 0.7619 (m-30) outliers start: 25 outliers final: 7 residues processed: 140 average time/residue: 1.2629 time to fit residues: 186.8236 Evaluate side-chains 131 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 123 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 74 optimal weight: 0.6980 chunk 61 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 97 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 292 ASN B 268 ASN N 123 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8085 Z= 0.166 Angle : 0.509 8.763 10968 Z= 0.265 Chirality : 0.041 0.246 1247 Planarity : 0.004 0.047 1400 Dihedral : 4.281 31.837 1119 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.87 % Allowed : 15.05 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: -0.23 (0.26), residues: 1002 helix: 1.29 (0.27), residues: 378 sheet: -0.51 (0.32), residues: 225 loop : -1.31 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.015 0.001 TYR N 60 ARG 0.004 0.000 ARG B 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 0.815 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7915 (tt0) REVERT: A 378 ASP cc_start: 0.7375 (m-30) cc_final: 0.7133 (m-30) REVERT: B 61 MET cc_start: 0.8547 (tmm) cc_final: 0.8054 (ptm) REVERT: B 246 ASP cc_start: 0.8001 (m-30) cc_final: 0.7664 (m-30) REVERT: G 20 LYS cc_start: 0.8970 (mttt) cc_final: 0.8755 (mttp) outliers start: 24 outliers final: 13 residues processed: 148 average time/residue: 1.1542 time to fit residues: 181.1421 Evaluate side-chains 136 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 223 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain A residue 356 ARG Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 8.9990 chunk 67 optimal weight: 0.0470 chunk 46 optimal weight: 0.4980 chunk 9 optimal weight: 2.9990 chunk 42 optimal weight: 0.0270 chunk 60 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 220 HIS A 292 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8085 Z= 0.168 Angle : 0.508 8.593 10968 Z= 0.262 Chirality : 0.041 0.183 1247 Planarity : 0.004 0.054 1400 Dihedral : 4.229 33.626 1119 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.27 % Allowed : 17.08 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.04 (0.27), residues: 1002 helix: 1.52 (0.28), residues: 379 sheet: -0.39 (0.32), residues: 225 loop : -1.17 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.017 0.001 TYR N 60 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8183 (mt-10) cc_final: 0.7925 (tt0) REVERT: B 61 MET cc_start: 0.8552 (tmm) cc_final: 0.8230 (ptm) REVERT: B 246 ASP cc_start: 0.7987 (m-30) cc_final: 0.7642 (m-30) outliers start: 19 outliers final: 11 residues processed: 136 average time/residue: 1.2070 time to fit residues: 173.8806 Evaluate side-chains 128 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 85 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8085 Z= 0.220 Angle : 0.529 8.481 10968 Z= 0.274 Chirality : 0.042 0.158 1247 Planarity : 0.004 0.063 1400 Dihedral : 4.324 33.998 1119 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.87 % Allowed : 16.97 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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 (0.27), residues: 1002 helix: 1.55 (0.28), residues: 381 sheet: -0.33 (0.32), residues: 225 loop : -1.03 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.018 0.001 TYR N 60 ARG 0.004 0.000 ARG A 347 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 125 time to evaluate : 2.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7982 (tt0) REVERT: B 9 GLN cc_start: 0.8639 (mm110) cc_final: 0.8237 (mm-40) REVERT: B 23 LYS cc_start: 0.8525 (mmpt) cc_final: 0.7861 (tmtm) REVERT: B 61 MET cc_start: 0.8595 (tmm) cc_final: 0.8319 (ptm) REVERT: B 246 ASP cc_start: 0.8007 (m-30) cc_final: 0.7657 (m-30) outliers start: 24 outliers final: 15 residues processed: 139 average time/residue: 1.2159 time to fit residues: 179.4339 Evaluate side-chains 138 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 123 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 32 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 79 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 292 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 8085 Z= 0.311 Angle : 0.589 8.685 10968 Z= 0.302 Chirality : 0.044 0.169 1247 Planarity : 0.005 0.069 1400 Dihedral : 4.543 35.485 1119 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 3.94 % Allowed : 16.85 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.10 (0.27), residues: 1002 helix: 1.46 (0.27), residues: 381 sheet: -0.29 (0.32), residues: 225 loop : -1.05 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 234 HIS 0.010 0.002 HIS A 357 PHE 0.015 0.001 PHE A 212 TYR 0.019 0.002 TYR N 60 ARG 0.009 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 129 time to evaluate : 1.023 Fit side-chains revert: symmetry clash REVERT: R 224 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7783 (ttm170) REVERT: A 314 GLU cc_start: 0.8284 (mt-10) cc_final: 0.8030 (tt0) REVERT: B 10 GLU cc_start: 0.7876 (tp30) cc_final: 0.6757 (tp30) REVERT: B 23 LYS cc_start: 0.8508 (mmpt) cc_final: 0.7840 (tmtm) REVERT: B 61 MET cc_start: 0.8599 (tmm) cc_final: 0.8274 (ptm) outliers start: 33 outliers final: 19 residues processed: 145 average time/residue: 1.1881 time to fit residues: 182.9125 Evaluate side-chains 145 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 125 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 224 ARG Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 92 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 95 optimal weight: 5.9990 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 292 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 17 GLN N 77 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 8085 Z= 0.229 Angle : 0.543 9.315 10968 Z= 0.280 Chirality : 0.042 0.161 1247 Planarity : 0.005 0.071 1400 Dihedral : 4.464 37.522 1119 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.99 % Allowed : 17.80 % Favored : 79.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.13 (0.27), residues: 1002 helix: 1.51 (0.27), residues: 385 sheet: -0.29 (0.32), residues: 226 loop : -1.09 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.007 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: R 107 ARG cc_start: 0.6793 (OUTLIER) cc_final: 0.6227 (ptp-170) REVERT: A 314 GLU cc_start: 0.8281 (mt-10) cc_final: 0.8019 (tt0) REVERT: B 23 LYS cc_start: 0.8495 (mmpt) cc_final: 0.7861 (tmtm) REVERT: B 61 MET cc_start: 0.8595 (tmm) cc_final: 0.8254 (ptm) REVERT: B 246 ASP cc_start: 0.7964 (m-30) cc_final: 0.7585 (m-30) REVERT: B 325 MET cc_start: 0.8496 (tpp) cc_final: 0.8114 (mmt) outliers start: 25 outliers final: 19 residues processed: 144 average time/residue: 1.2308 time to fit residues: 188.0665 Evaluate side-chains 146 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 126 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain R residue 219 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 310 ILE Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain N residue 93 VAL Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 56 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 60 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8085 Z= 0.160 Angle : 0.503 9.248 10968 Z= 0.259 Chirality : 0.041 0.150 1247 Planarity : 0.004 0.072 1400 Dihedral : 4.217 33.843 1119 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.03 % Allowed : 19.47 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.25 (0.27), residues: 1002 helix: 1.62 (0.27), residues: 385 sheet: -0.21 (0.32), residues: 225 loop : -1.04 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.018 0.001 TYR N 60 ARG 0.007 0.000 ARG R 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 137 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8255 (mt-10) cc_final: 0.7992 (tt0) REVERT: B 23 LYS cc_start: 0.8550 (mmpt) cc_final: 0.7907 (tmtm) REVERT: B 61 MET cc_start: 0.8584 (tmm) cc_final: 0.8303 (ptm) REVERT: B 246 ASP cc_start: 0.8019 (m-30) cc_final: 0.7621 (m-30) REVERT: B 325 MET cc_start: 0.8542 (tpp) cc_final: 0.8174 (tpt) outliers start: 17 outliers final: 15 residues processed: 148 average time/residue: 1.1859 time to fit residues: 185.9691 Evaluate side-chains 144 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 9.9990 chunk 91 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 80 optimal weight: 0.9980 chunk 84 optimal weight: 0.0000 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 77 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.2362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 8085 Z= 0.158 Angle : 0.512 9.388 10968 Z= 0.262 Chirality : 0.041 0.146 1247 Planarity : 0.004 0.073 1400 Dihedral : 4.164 32.694 1119 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.39 % Allowed : 20.43 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.40 (0.27), residues: 1002 helix: 1.73 (0.27), residues: 379 sheet: -0.08 (0.32), residues: 223 loop : -0.93 (0.31), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.012 0.001 PHE A 212 TYR 0.019 0.001 TYR N 60 ARG 0.008 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 136 time to evaluate : 0.912 Fit side-chains revert: symmetry clash REVERT: R 45 LEU cc_start: 0.7354 (mp) cc_final: 0.6702 (tt) REVERT: R 107 ARG cc_start: 0.6897 (OUTLIER) cc_final: 0.6380 (ptp-170) REVERT: A 314 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7956 (tt0) REVERT: B 23 LYS cc_start: 0.8516 (mmpt) cc_final: 0.7895 (tmtm) REVERT: B 61 MET cc_start: 0.8592 (tmm) cc_final: 0.8304 (ptm) REVERT: B 246 ASP cc_start: 0.7966 (m-30) cc_final: 0.7588 (m-30) REVERT: B 325 MET cc_start: 0.8492 (tpp) cc_final: 0.8198 (tpt) outliers start: 20 outliers final: 17 residues processed: 149 average time/residue: 1.2206 time to fit residues: 192.4770 Evaluate side-chains 150 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 132 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain R residue 318 LEU Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 98 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 83 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN N 77 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8085 Z= 0.239 Angle : 0.576 10.359 10968 Z= 0.291 Chirality : 0.043 0.161 1247 Planarity : 0.005 0.073 1400 Dihedral : 4.494 35.770 1119 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.03 % Allowed : 20.67 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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 (0.26), residues: 1002 helix: 1.61 (0.27), residues: 378 sheet: -0.17 (0.32), residues: 226 loop : -0.96 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.008 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.023 0.001 TYR N 60 ARG 0.008 0.000 ARG A 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2004 Ramachandran restraints generated. 1002 Oldfield, 0 Emsley, 1002 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 127 time to evaluate : 0.810 Fit side-chains revert: symmetry clash REVERT: R 45 LEU cc_start: 0.7372 (mp) cc_final: 0.6800 (tt) REVERT: R 107 ARG cc_start: 0.6862 (OUTLIER) cc_final: 0.6312 (ptp-170) REVERT: A 314 GLU cc_start: 0.8237 (mt-10) cc_final: 0.8010 (tt0) REVERT: B 13 GLN cc_start: 0.7670 (tt0) cc_final: 0.7329 (tm-30) REVERT: B 23 LYS cc_start: 0.8554 (mmpt) cc_final: 0.7892 (tmtm) REVERT: B 61 MET cc_start: 0.8616 (tmm) cc_final: 0.8366 (ptm) REVERT: B 246 ASP cc_start: 0.7931 (m-30) cc_final: 0.7554 (m-30) REVERT: B 325 MET cc_start: 0.8602 (tpp) cc_final: 0.8307 (tpt) outliers start: 17 outliers final: 16 residues processed: 138 average time/residue: 1.2277 time to fit residues: 179.3091 Evaluate side-chains 142 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 107 ARG Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 271 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 340 ASN Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 72 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.4980 chunk 78 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 69 optimal weight: 6.9990 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN N 77 ASN N 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.125969 restraints weight = 9371.988| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.26 r_work: 0.3285 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8085 Z= 0.168 Angle : 0.536 10.362 10968 Z= 0.270 Chirality : 0.041 0.147 1247 Planarity : 0.004 0.072 1400 Dihedral : 4.274 33.437 1119 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.15 % Allowed : 20.79 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % 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: 0.36 (0.26), residues: 1002 helix: 1.68 (0.27), residues: 379 sheet: -0.12 (0.32), residues: 225 loop : -0.92 (0.31), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.005 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.021 0.001 TYR N 60 ARG 0.007 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3553.00 seconds wall clock time: 63 minutes 42.61 seconds (3822.61 seconds total)