Starting phenix.real_space_refine on Tue Feb 13 22:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx3_30490/02_2024/7cx3_30490_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx3_30490/02_2024/7cx3_30490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx3_30490/02_2024/7cx3_30490.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx3_30490/02_2024/7cx3_30490.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx3_30490/02_2024/7cx3_30490_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cx3_30490/02_2024/7cx3_30490_updated.pdb" } resolution = 2.8 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= 0.013 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 5023 2.51 5 N 1373 2.21 5 O 1474 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R GLU 105": "OE1" <-> "OE2" Residue "R ARG 107": "NH1" <-> "NH2" Residue "R PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 150": "NH1" <-> "NH2" Residue "R ARG 190": "NH1" <-> "NH2" Residue "R ASP 261": "OD1" <-> "OD2" Residue "R TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 319": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A GLU 27": "OE1" <-> "OE2" Residue "A ASP 223": "OD1" <-> "OD2" Residue "A ARG 228": "NH1" <-> "NH2" Residue "A ASP 229": "OD1" <-> "OD2" Residue "A ARG 265": "NH1" <-> "NH2" Residue "A ASP 295": "OD1" <-> "OD2" Residue "A GLU 314": "OE1" <-> "OE2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A GLU 322": "OE1" <-> "OE2" Residue "A ARG 333": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ASP 378": "OD1" <-> "OD2" Residue "A ARG 389": "NH1" <-> "NH2" Residue "A GLU 392": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B ASP 5": "OD1" <-> "OD2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B GLU 12": "OE1" <-> "OE2" 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 ARG 137": "NH1" <-> "NH2" Residue "B ASP 170": "OD1" <-> "OD2" Residue "B ARG 197": "NH1" <-> "NH2" Residue "B ASP 212": "OD1" <-> "OD2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "G ARG 13": "NH1" <-> "NH2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" 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-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7923 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2012 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2012 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 11, 'TRANS': 253} 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: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'GNO': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.99, per 1000 atoms: 0.63 Number of scatterers: 7923 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 1474 8.00 N 1373 7.00 C 5023 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=2.03 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: 3.15 Conformation dependent library (CDL) restraints added in 1.5 seconds 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 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: 27 helices and 11 sheets defined 36.8% alpha, 20.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'R' and resid 28 through 44 Processing helix chain 'R' and resid 66 through 94 Proline residue: R 87 - end of helix removed outlier: 4.016A pdb=" N SER R 92 " --> pdb=" O VAL R 88 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N TYR R 93 " --> pdb=" O VAL R 89 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALA R 94 " --> pdb=" O LEU R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 139 Processing helix chain 'R' and resid 141 through 147 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: 3.836A pdb=" N LEU R 157 " --> pdb=" O LEU R 154 " (cutoff:3.500A) Proline residue: R 158 - end of helix removed outlier: 3.791A pdb=" N TYR R 161 " --> pdb=" O PRO R 158 " (cutoff:3.500A) Processing helix chain 'R' and resid 171 through 173 No H-bonds generated for 'chain 'R' and resid 171 through 173' Processing helix chain 'R' and resid 196 through 228 Processing helix chain 'R' and resid 259 through 275 Processing helix chain 'R' and resid 278 through 284 Processing helix chain 'R' and resid 288 through 294 removed outlier: 3.551A pdb=" N LYS R 293 " --> pdb=" O THR R 289 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU R 294 " --> pdb=" O SER R 290 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 316 removed outlier: 3.760A pdb=" N LEU R 301 " --> pdb=" O ASP R 297 " (cutoff:3.500A) removed outlier: 3.706A 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 13 through 39 removed outlier: 3.603A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 59 Processing helix chain 'A' and resid 235 through 238 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 282 through 284 No H-bonds generated for 'chain 'A' and resid 282 through 284' Processing helix chain 'A' and resid 294 through 303 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: 3.933A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 391 removed outlier: 4.114A pdb=" N GLN A 390 " --> pdb=" O MET A 386 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 25 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: 4.458A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.798A 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 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' 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: 7.055A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.095A 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: 6.750A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.993A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.457A 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: 6.960A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.439A 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: 6.574A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.160A 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: 7.004A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.374A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.260A 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: 6.669A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.967A 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: 3.845A 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: 6.634A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.428A 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: 6.243A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 361 hydrogen bonds defined for protein. 1011 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: 2.36 Time building geometry restraints manager: 3.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1460 1.33 - 1.45: 2083 1.45 - 1.57: 4464 1.57 - 1.69: 0 1.69 - 1.81: 76 Bond restraints: 8083 Sorted by residual: bond pdb=" C16 GNO R 401 " pdb=" C9 GNO R 401 " ideal model delta sigma weight residual 1.386 1.527 -0.141 2.00e-02 2.50e+03 4.95e+01 bond pdb=" C12 GNO R 401 " pdb=" C7 GNO R 401 " ideal model delta sigma weight residual 1.387 1.527 -0.140 2.00e-02 2.50e+03 4.89e+01 bond pdb=" C4 GNO R 401 " pdb=" C8 GNO R 401 " ideal model delta sigma weight residual 1.386 1.525 -0.139 2.00e-02 2.50e+03 4.81e+01 bond pdb=" C3 GNO R 401 " pdb=" C6 GNO R 401 " ideal model delta sigma weight residual 1.392 1.527 -0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C10 GNO R 401 " pdb=" C11 GNO R 401 " ideal model delta sigma weight residual 1.392 1.526 -0.134 2.00e-02 2.50e+03 4.49e+01 ... (remaining 8078 not shown) Histogram of bond angle deviations from ideal: 99.27 - 106.24: 167 106.24 - 113.20: 4356 113.20 - 120.17: 2941 120.17 - 127.14: 3418 127.14 - 134.11: 82 Bond angle restraints: 10964 Sorted by residual: angle pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" C ALA A 351 " ideal model delta sigma weight residual 111.36 126.41 -15.05 1.09e+00 8.42e-01 1.91e+02 angle pdb=" N SER A 352 " pdb=" CA SER A 352 " pdb=" C SER A 352 " ideal model delta sigma weight residual 111.07 120.76 -9.69 1.07e+00 8.73e-01 8.20e+01 angle pdb=" N THR A 350 " pdb=" CA THR A 350 " pdb=" C THR A 350 " ideal model delta sigma weight residual 111.36 119.57 -8.21 1.09e+00 8.42e-01 5.67e+01 angle pdb=" N ASP A 354 " pdb=" CA ASP A 354 " pdb=" C ASP A 354 " ideal model delta sigma weight residual 111.28 118.75 -7.47 1.09e+00 8.42e-01 4.69e+01 angle pdb=" O1 GNO R 401 " pdb=" S1 GNO R 401 " pdb=" O2 GNO R 401 " ideal model delta sigma weight residual 120.12 101.78 18.34 3.00e+00 1.11e-01 3.74e+01 ... (remaining 10959 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 4438 17.95 - 35.90: 314 35.90 - 53.85: 48 53.85 - 71.80: 8 71.80 - 89.76: 4 Dihedral angle restraints: 4812 sinusoidal: 1844 harmonic: 2968 Sorted by residual: dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual -180.00 -155.28 -24.72 0 5.00e+00 4.00e-02 2.45e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 158.94 21.06 0 5.00e+00 4.00e-02 1.77e+01 dihedral pdb=" C ALA A 351 " pdb=" N ALA A 351 " pdb=" CA ALA A 351 " pdb=" CB ALA A 351 " ideal model delta harmonic sigma weight residual -122.60 -132.76 10.16 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 4809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.105: 1197 0.105 - 0.210: 42 0.210 - 0.315: 7 0.315 - 0.420: 0 0.420 - 0.525: 1 Chirality restraints: 1247 Sorted by residual: chirality pdb=" CA ALA A 351 " pdb=" N ALA A 351 " pdb=" C ALA A 351 " pdb=" CB ALA A 351 " both_signs ideal model delta sigma weight residual False 2.48 1.96 0.53 2.00e-01 2.50e+01 6.90e+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 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA SER A 352 " pdb=" N SER A 352 " pdb=" C SER A 352 " pdb=" CB SER A 352 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 ... (remaining 1244 not shown) Planarity restraints: 1400 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 349 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER A 349 " -0.062 2.00e-02 2.50e+03 pdb=" O SER A 349 " 0.023 2.00e-02 2.50e+03 pdb=" N THR A 350 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 59 " -0.017 2.00e-02 2.50e+03 1.56e-02 4.88e+00 pdb=" CG TYR B 59 " 0.038 2.00e-02 2.50e+03 pdb=" CD1 TYR B 59 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR B 59 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR B 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 59 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR B 59 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 59 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " 0.026 5.00e-02 4.00e+02 3.91e-02 2.45e+00 pdb=" N PRO B 236 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " 0.022 5.00e-02 4.00e+02 ... (remaining 1397 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 107 2.67 - 3.23: 7262 3.23 - 3.78: 12017 3.78 - 4.34: 17154 4.34 - 4.90: 28431 Nonbonded interactions: 64971 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.109 2.440 nonbonded pdb=" OD1 ASN A 292 " pdb=" OG1 THR A 364 " model vdw 2.232 2.440 nonbonded pdb=" OE2 GLU A 330 " pdb=" OG1 THR A 335 " model vdw 2.242 2.440 nonbonded pdb=" O CYS B 204 " pdb=" OH TYR N 117 " model vdw 2.255 2.440 nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.290 2.440 ... (remaining 64966 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: 0.430 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: 1.850 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.870 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 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 : 0.006 0.141 8083 Z= 0.422 Angle : 0.664 18.338 10964 Z= 0.407 Chirality : 0.049 0.525 1247 Planarity : 0.004 0.039 1400 Dihedral : 12.663 89.755 2881 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % 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: -1.96 (0.24), residues: 1001 helix: -0.57 (0.23), residues: 383 sheet: -0.63 (0.32), residues: 219 loop : -2.37 (0.27), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.038 0.002 TYR B 59 ARG 0.002 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 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: 0 poor density : 158 time to evaluate : 0.909 Fit side-chains REVERT: R 27 ILE cc_start: 0.7262 (mt) cc_final: 0.7023 (tt) REVERT: A 343 ASP cc_start: 0.7603 (m-30) cc_final: 0.7263 (m-30) REVERT: A 386 MET cc_start: 0.7647 (ttm) cc_final: 0.7222 (mtp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 1.3683 time to fit residues: 227.1433 Evaluate side-chains 125 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 3.9990 chunk 75 optimal weight: 0.0670 chunk 41 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 50 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 overall best weight: 0.8922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8083 Z= 0.171 Angle : 0.506 10.125 10964 Z= 0.265 Chirality : 0.042 0.150 1247 Planarity : 0.004 0.046 1400 Dihedral : 4.545 41.561 1120 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.03 % Allowed : 10.87 % Favored : 87.10 % 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: -0.77 (0.25), residues: 1001 helix: 0.70 (0.26), residues: 395 sheet: -0.25 (0.34), residues: 215 loop : -1.91 (0.28), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR B 124 ARG 0.005 0.000 ARG R 302 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 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: 17 poor density : 125 time to evaluate : 0.847 Fit side-chains REVERT: A 343 ASP cc_start: 0.7567 (m-30) cc_final: 0.7158 (m-30) REVERT: A 386 MET cc_start: 0.7568 (ttm) cc_final: 0.7331 (mtp) REVERT: B 322 ASP cc_start: 0.7968 (t0) cc_final: 0.7650 (m-30) REVERT: G 14 LYS cc_start: 0.8394 (ttpt) cc_final: 0.7507 (tttp) REVERT: N 105 ARG cc_start: 0.7634 (OUTLIER) cc_final: 0.7132 (ptt180) outliers start: 17 outliers final: 9 residues processed: 132 average time/residue: 1.3824 time to fit residues: 191.7237 Evaluate side-chains 128 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 9.9990 chunk 27 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 24 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 97 optimal weight: 0.5980 chunk 80 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 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 220 HIS A 390 GLN B 17 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8083 Z= 0.227 Angle : 0.528 7.530 10964 Z= 0.276 Chirality : 0.042 0.151 1247 Planarity : 0.004 0.049 1400 Dihedral : 4.444 32.761 1120 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.51 % Allowed : 13.86 % Favored : 83.63 % 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: -0.29 (0.26), residues: 1001 helix: 1.14 (0.26), residues: 391 sheet: 0.09 (0.35), residues: 220 loop : -1.75 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 234 HIS 0.009 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR B 124 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 124 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 343 ASP cc_start: 0.7557 (m-30) cc_final: 0.7190 (m-30) REVERT: A 386 MET cc_start: 0.7733 (ttm) cc_final: 0.7441 (mtp) REVERT: B 9 GLN cc_start: 0.6795 (mm110) cc_final: 0.6539 (mm110) REVERT: B 186 ASP cc_start: 0.7688 (m-30) cc_final: 0.7443 (m-30) REVERT: B 322 ASP cc_start: 0.8066 (t0) cc_final: 0.7729 (m-30) REVERT: G 14 LYS cc_start: 0.8388 (ttpt) cc_final: 0.7457 (tttp) REVERT: N 105 ARG cc_start: 0.7545 (OUTLIER) cc_final: 0.7085 (ptt180) outliers start: 21 outliers final: 15 residues processed: 134 average time/residue: 1.4648 time to fit residues: 206.2200 Evaluate side-chains 137 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 42 ARG Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Chi-restraints excluded: chain N residue 125 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 46 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 85 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 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 390 GLN B 17 GLN B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8083 Z= 0.163 Angle : 0.480 7.236 10964 Z= 0.252 Chirality : 0.041 0.145 1247 Planarity : 0.004 0.047 1400 Dihedral : 4.173 36.468 1120 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.75 % Allowed : 15.29 % Favored : 81.96 % 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: 0.10 (0.26), residues: 1001 helix: 1.47 (0.27), residues: 393 sheet: 0.22 (0.35), residues: 218 loop : -1.50 (0.29), residues: 390 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 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR B 124 ARG 0.007 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 130 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: R 190 ARG cc_start: 0.7568 (ttp-110) cc_final: 0.6447 (ptp-170) REVERT: A 265 ARG cc_start: 0.7381 (mtp85) cc_final: 0.7048 (mtm110) REVERT: A 343 ASP cc_start: 0.7498 (m-30) cc_final: 0.7084 (m-30) REVERT: A 386 MET cc_start: 0.7649 (ttm) cc_final: 0.7371 (mtp) REVERT: B 9 GLN cc_start: 0.6839 (mm110) cc_final: 0.6565 (mm110) REVERT: B 186 ASP cc_start: 0.7591 (m-30) cc_final: 0.7349 (m-30) REVERT: B 322 ASP cc_start: 0.8158 (t0) cc_final: 0.7809 (m-30) REVERT: G 14 LYS cc_start: 0.8416 (ttpt) cc_final: 0.7510 (tttp) REVERT: G 27 ARG cc_start: 0.8894 (mtt90) cc_final: 0.8475 (mtt90) REVERT: N 105 ARG cc_start: 0.7416 (OUTLIER) cc_final: 0.7052 (ptt180) outliers start: 23 outliers final: 13 residues processed: 143 average time/residue: 1.4426 time to fit residues: 216.8674 Evaluate side-chains 130 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG 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: 0.9980 chunk 54 optimal weight: 4.9990 chunk 1 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 48 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 17 GLN B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8083 Z= 0.458 Angle : 0.661 10.779 10964 Z= 0.343 Chirality : 0.048 0.192 1247 Planarity : 0.005 0.079 1400 Dihedral : 4.747 35.883 1120 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.35 % Allowed : 15.89 % Favored : 80.76 % 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: -0.08 (0.26), residues: 1001 helix: 1.20 (0.26), residues: 394 sheet: 0.17 (0.35), residues: 225 loop : -1.51 (0.29), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP A 234 HIS 0.013 0.002 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.018 0.002 TYR B 105 ARG 0.007 0.001 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 117 time to evaluate : 0.960 Fit side-chains revert: symmetry clash REVERT: R 190 ARG cc_start: 0.7696 (ttp-110) cc_final: 0.6598 (ptp-170) REVERT: A 265 ARG cc_start: 0.7508 (mtp85) cc_final: 0.7226 (mtm110) REVERT: A 343 ASP cc_start: 0.7571 (m-30) cc_final: 0.7223 (m-30) REVERT: B 9 GLN cc_start: 0.6937 (mm110) cc_final: 0.6655 (mm110) REVERT: B 59 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7806 (t80) REVERT: N 105 ARG cc_start: 0.7444 (OUTLIER) cc_final: 0.6898 (ptt180) outliers start: 28 outliers final: 17 residues processed: 130 average time/residue: 1.4271 time to fit residues: 195.0442 Evaluate side-chains 132 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG 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: 2.9990 chunk 86 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 17 GLN B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8083 Z= 0.182 Angle : 0.516 9.508 10964 Z= 0.268 Chirality : 0.042 0.165 1247 Planarity : 0.004 0.047 1400 Dihedral : 4.314 36.037 1120 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.11 % Allowed : 17.32 % Favored : 79.57 % 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: 0.25 (0.26), residues: 1001 helix: 1.56 (0.26), residues: 393 sheet: 0.38 (0.35), residues: 219 loop : -1.44 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 82 HIS 0.006 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR B 124 ARG 0.006 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: R 190 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.6587 (ptp-170) REVERT: A 265 ARG cc_start: 0.7384 (mtp85) cc_final: 0.7142 (mtm110) REVERT: A 343 ASP cc_start: 0.7525 (m-30) cc_final: 0.7140 (m-30) REVERT: B 9 GLN cc_start: 0.6793 (mm110) cc_final: 0.6528 (mm110) REVERT: B 59 TYR cc_start: 0.8791 (OUTLIER) cc_final: 0.7756 (t80) REVERT: N 105 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.7066 (ptt180) outliers start: 26 outliers final: 20 residues processed: 137 average time/residue: 1.4370 time to fit residues: 207.0357 Evaluate side-chains 136 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 114 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 224 ARG Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 268 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 35 GLN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG 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: 3.9990 chunk 54 optimal weight: 6.9990 chunk 69 optimal weight: 0.3980 chunk 80 optimal weight: 0.2980 chunk 53 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 5.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 17 GLN B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8083 Z= 0.136 Angle : 0.495 10.135 10964 Z= 0.252 Chirality : 0.041 0.143 1247 Planarity : 0.004 0.047 1400 Dihedral : 4.027 38.701 1120 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.46 % Allowed : 17.56 % Favored : 78.97 % 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: 0.61 (0.27), residues: 1001 helix: 1.86 (0.27), residues: 393 sheet: 0.48 (0.35), residues: 217 loop : -1.18 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR B 124 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 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: 29 poor density : 128 time to evaluate : 0.972 Fit side-chains revert: symmetry clash REVERT: R 190 ARG cc_start: 0.7782 (ttp-110) cc_final: 0.6663 (ptp-170) REVERT: A 60 MET cc_start: 0.8155 (mtp) cc_final: 0.7653 (mtm) REVERT: A 265 ARG cc_start: 0.7332 (mtp85) cc_final: 0.7084 (mtm110) REVERT: A 343 ASP cc_start: 0.7450 (m-30) cc_final: 0.7007 (m-30) REVERT: B 59 TYR cc_start: 0.8777 (OUTLIER) cc_final: 0.7773 (t80) REVERT: G 14 LYS cc_start: 0.8440 (ttpt) cc_final: 0.7514 (tttp) REVERT: N 105 ARG cc_start: 0.7424 (OUTLIER) cc_final: 0.7066 (ptt180) outliers start: 29 outliers final: 17 residues processed: 142 average time/residue: 1.3056 time to fit residues: 195.6128 Evaluate side-chains 143 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG 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: 1.9990 chunk 28 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 60 optimal weight: 0.0050 chunk 65 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 86 optimal weight: 0.0040 chunk 91 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8083 Z= 0.128 Angle : 0.497 10.076 10964 Z= 0.252 Chirality : 0.040 0.140 1247 Planarity : 0.004 0.047 1400 Dihedral : 3.884 38.399 1120 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.87 % Allowed : 18.88 % Favored : 78.26 % 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: 0.79 (0.27), residues: 1001 helix: 1.98 (0.27), residues: 394 sheet: 0.59 (0.35), residues: 215 loop : -1.05 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.004 0.001 HIS A 357 PHE 0.029 0.001 PHE R 143 TYR 0.010 0.001 TYR B 124 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 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: 24 poor density : 131 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 154 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7270 (mm) REVERT: A 60 MET cc_start: 0.8129 (mtp) cc_final: 0.7638 (mtm) REVERT: A 216 LYS cc_start: 0.8646 (mttm) cc_final: 0.8389 (mttp) REVERT: A 343 ASP cc_start: 0.7486 (m-30) cc_final: 0.7038 (m-30) REVERT: A 386 MET cc_start: 0.7734 (ttm) cc_final: 0.7395 (mtp) REVERT: B 59 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.7734 (t80) REVERT: G 14 LYS cc_start: 0.8442 (ttpt) cc_final: 0.7509 (tttp) REVERT: N 105 ARG cc_start: 0.7428 (OUTLIER) cc_final: 0.7100 (ptt180) outliers start: 24 outliers final: 18 residues processed: 147 average time/residue: 1.2232 time to fit residues: 190.2701 Evaluate side-chains 140 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 119 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain R residue 225 MET Chi-restraints excluded: chain R residue 275 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 105 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.0670 chunk 91 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 38 optimal weight: 0.0770 chunk 69 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 80 optimal weight: 0.0770 chunk 84 optimal weight: 9.9990 chunk 58 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 57 optimal weight: 5.9990 overall best weight: 0.2834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 176 GLN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.2311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8083 Z= 0.113 Angle : 0.490 10.634 10964 Z= 0.248 Chirality : 0.040 0.136 1247 Planarity : 0.004 0.046 1400 Dihedral : 3.793 43.161 1120 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.15 % Allowed : 20.07 % Favored : 77.78 % 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: 0.97 (0.27), residues: 1001 helix: 2.24 (0.27), residues: 388 sheet: 0.44 (0.35), residues: 228 loop : -0.90 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.000 HIS A 357 PHE 0.013 0.001 PHE A 212 TYR 0.009 0.001 TYR B 124 ARG 0.004 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 116 MET cc_start: 0.7165 (ttm) cc_final: 0.6935 (ttm) REVERT: R 154 LEU cc_start: 0.7383 (OUTLIER) cc_final: 0.7161 (mm) REVERT: A 60 MET cc_start: 0.8100 (mtp) cc_final: 0.7742 (mtm) REVERT: A 343 ASP cc_start: 0.7507 (m-30) cc_final: 0.7058 (m-30) REVERT: A 386 MET cc_start: 0.7766 (ttm) cc_final: 0.7377 (mtp) REVERT: G 14 LYS cc_start: 0.8436 (ttpt) cc_final: 0.7509 (tttp) REVERT: G 27 ARG cc_start: 0.8627 (mtt90) cc_final: 0.8359 (mtt90) REVERT: N 105 ARG cc_start: 0.7430 (ptt180) cc_final: 0.7123 (ptt180) outliers start: 18 outliers final: 11 residues processed: 141 average time/residue: 1.3586 time to fit residues: 202.1869 Evaluate side-chains 135 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS 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: 0.7980 chunk 65 optimal weight: 7.9990 chunk 98 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 78 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 62 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 24 optimal weight: 10.0000 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 176 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.2233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8083 Z= 0.260 Angle : 0.578 11.131 10964 Z= 0.295 Chirality : 0.043 0.144 1247 Planarity : 0.004 0.046 1400 Dihedral : 4.195 40.856 1120 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.27 % Allowed : 20.19 % Favored : 77.54 % 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: 0.76 (0.27), residues: 1001 helix: 1.94 (0.26), residues: 394 sheet: 0.56 (0.35), residues: 219 loop : -1.07 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.008 0.001 HIS A 357 PHE 0.027 0.002 PHE R 143 TYR 0.016 0.002 TYR B 124 ARG 0.006 0.000 ARG A 356 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2002 Ramachandran restraints generated. 1001 Oldfield, 0 Emsley, 1001 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 154 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7224 (mm) REVERT: A 35 GLN cc_start: 0.7933 (tt0) cc_final: 0.7606 (tt0) REVERT: A 216 LYS cc_start: 0.8695 (mttm) cc_final: 0.8475 (mmtp) REVERT: A 265 ARG cc_start: 0.7349 (mtp85) cc_final: 0.7112 (mtm110) REVERT: A 343 ASP cc_start: 0.7509 (m-30) cc_final: 0.7102 (m-30) REVERT: B 186 ASP cc_start: 0.7800 (m-30) cc_final: 0.7593 (m-30) REVERT: B 322 ASP cc_start: 0.8050 (t0) cc_final: 0.7803 (m-30) outliers start: 19 outliers final: 17 residues processed: 134 average time/residue: 1.4140 time to fit residues: 199.3054 Evaluate side-chains 141 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 123 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 109 CYS Chi-restraints excluded: chain R residue 154 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 163 VAL Chi-restraints excluded: chain R residue 189 ILE Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 250 SER Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain N residue 59 SER Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 99 CYS 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: 4.9990 chunk 11 optimal weight: 10.0000 chunk 21 optimal weight: 6.9990 chunk 78 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 chunk 69 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN B 44 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.173147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.117837 restraints weight = 8677.510| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.12 r_work: 0.3189 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 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 : 0.006 0.044 8083 Z= 0.363 Angle : 0.631 10.987 10964 Z= 0.324 Chirality : 0.045 0.144 1247 Planarity : 0.005 0.057 1400 Dihedral : 4.497 37.393 1120 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.87 % Allowed : 20.07 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.27), residues: 1001 helix: 1.75 (0.26), residues: 387 sheet: 0.27 (0.35), residues: 224 loop : -1.09 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.011 0.002 HIS A 357 PHE 0.017 0.002 PHE A 212 TYR 0.018 0.002 TYR N 95 ARG 0.006 0.000 ARG A 356 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3745.03 seconds wall clock time: 67 minutes 0.96 seconds (4020.96 seconds total)