Starting phenix.real_space_refine on Fri Feb 16 12:43:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/02_2024/7ckz_30395_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/02_2024/7ckz_30395.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/02_2024/7ckz_30395.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/02_2024/7ckz_30395.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/02_2024/7ckz_30395_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ckz_30395/02_2024/7ckz_30395_updated.pdb" } resolution = 3.1 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7222 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 53 5.16 5 Cl 2 4.86 5 C 5180 2.51 5 N 1406 2.21 5 O 1492 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A GLU 15": "OE1" <-> "OE2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A GLU 21": "OE1" <-> "OE2" Residue "A ARG 42": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "B GLU 3": "OE1" <-> "OE2" Residue "B GLU 10": "OE1" <-> "OE2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B GLU 138": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 260": "OE1" <-> "OE2" Residue "G GLU 22": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "N GLU 46": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N ARG 98": "NH1" <-> "NH2" Residue "R GLU 132": "OE1" <-> "OE2" Residue "R ARG 227": "NH1" <-> "NH2" Residue "R GLU 232": "OE1" <-> "OE2" 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: 8133 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1906 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 6, 'TRANS': 229} Chain breaks: 2 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 69 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2587 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 22 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: 970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 970 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2232 Unusual residues: {'CLR': 1, 'G4C': 1, 'LDP': 1} Classifications: {'peptide': 275, 'undetermined': 3} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 9, 'TRANS': 265, None: 3} Not linked: pdbres="LEU R 344 " pdbres="CLR R 501 " Not linked: pdbres="CLR R 501 " pdbres="LDP R 502 " Not linked: pdbres="LDP R 502 " pdbres="G4C R 503 " Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 43 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 4.99, per 1000 atoms: 0.61 Number of scatterers: 8133 At special positions: 0 Unit cell: (96, 80, 125, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Cl 2 17.00 S 53 16.00 O 1492 8.00 N 1406 7.00 C 5180 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 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 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.02 Simple disulfide: pdb=" SG CYS R 298 " - pdb=" SG CYS R 307 " 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: 3.24 Conformation dependent library (CDL) restraints added in 1.6 seconds 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 11 sheets defined 37.4% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 15 through 39 removed outlier: 3.864A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 58 Processing helix chain 'A' and resid 234 through 237 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 300 removed outlier: 4.357A pdb=" N GLU A 299 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 332 through 349 removed outlier: 3.756A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 30 through 32 No H-bonds generated for 'chain 'B' and resid 30 through 32' Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.769A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'R' and resid 23 through 49 Processing helix chain 'R' and resid 58 through 75 removed outlier: 4.464A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 87 Processing helix chain 'R' and resid 93 through 126 removed outlier: 3.603A pdb=" N CYS R 96 " --> pdb=" O GLY R 93 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ASN R 97 " --> pdb=" O SER R 94 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR R 108 " --> pdb=" O MET R 105 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER R 126 " --> pdb=" O TRP R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 134 Processing helix chain 'R' and resid 137 through 160 removed outlier: 4.621A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 192 through 202 removed outlier: 3.849A pdb=" N SER R 197 " --> pdb=" O THR R 193 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N VAL R 200 " --> pdb=" O ILE R 196 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ILE R 201 " --> pdb=" O SER R 197 " (cutoff:3.500A) Processing helix chain 'R' and resid 204 through 236 removed outlier: 4.324A pdb=" N ALA R 234 " --> pdb=" O ALA R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 264 through 277 removed outlier: 4.016A pdb=" N LYS R 269 " --> pdb=" O LYS R 265 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LEU R 271 " --> pdb=" O GLU R 267 " (cutoff:3.500A) Processing helix chain 'R' and resid 279 through 292 Proline residue: R 287 - end of helix removed outlier: 3.882A pdb=" N LEU R 291 " --> pdb=" O PRO R 287 " (cutoff:3.500A) Processing helix chain 'R' and resid 310 through 330 removed outlier: 4.129A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N PHE R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 335 through 343 removed outlier: 3.932A pdb=" N ALA R 340 " --> pdb=" O ASP R 336 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N THR R 343 " --> pdb=" O LYS R 339 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 286 through 292 removed outlier: 3.505A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.581A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 102 through 105 removed outlier: 4.039A pdb=" N GLY B 115 " --> pdb=" O THR B 102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 178 through 181 removed outlier: 3.563A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.774A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.733A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE B 222 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.364A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N SER B 245 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 294 through 298 Processing sheet with id= H, first strand: chain 'B' and resid 317 through 320 removed outlier: 3.830A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 121 through 125 removed outlier: 5.474A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.701A pdb=" N LEU N 20 " --> pdb=" O LEU N 81 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU N 81 " --> pdb=" O LEU N 20 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.503A pdb=" N GLY N 10 " --> pdb=" O GLN N 123 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.114A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 957 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: 2.73 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1304 1.31 - 1.44: 2324 1.44 - 1.57: 4601 1.57 - 1.70: 1 1.70 - 1.82: 74 Bond restraints: 8304 Sorted by residual: bond pdb=" C05 G4C R 503 " pdb=" N04 G4C R 503 " ideal model delta sigma weight residual 1.355 1.481 -0.126 2.00e-02 2.50e+03 3.96e+01 bond pdb=" C16 G4C R 503 " pdb=" C18 G4C R 503 " ideal model delta sigma weight residual 1.508 1.594 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" N ARG N 105 " pdb=" CA ARG N 105 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.18e-02 7.18e+03 7.80e+00 bond pdb=" N PHE B 234 " pdb=" CA PHE B 234 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.25e-02 6.40e+03 6.34e+00 bond pdb=" C08 G4C R 503 " pdb="CL9 G4C R 503 " ideal model delta sigma weight residual 1.735 1.785 -0.050 2.00e-02 2.50e+03 6.18e+00 ... (remaining 8299 not shown) Histogram of bond angle deviations from ideal: 100.15 - 106.93: 186 106.93 - 113.71: 4632 113.71 - 120.48: 3253 120.48 - 127.26: 3110 127.26 - 134.04: 89 Bond angle restraints: 11270 Sorted by residual: angle pdb=" C03 G4C R 503 " pdb=" N04 G4C R 503 " pdb=" C05 G4C R 503 " ideal model delta sigma weight residual 118.75 128.13 -9.38 3.00e+00 1.11e-01 9.77e+00 angle pdb=" N ARG N 105 " pdb=" CA ARG N 105 " pdb=" C ARG N 105 " ideal model delta sigma weight residual 112.72 109.57 3.15 1.14e+00 7.69e-01 7.61e+00 angle pdb=" N VAL R 276 " pdb=" CA VAL R 276 " pdb=" C VAL R 276 " ideal model delta sigma weight residual 111.81 109.50 2.31 8.60e-01 1.35e+00 7.24e+00 angle pdb=" C06 G4C R 503 " pdb=" C05 G4C R 503 " pdb=" N04 G4C R 503 " ideal model delta sigma weight residual 116.82 124.06 -7.24 3.00e+00 1.11e-01 5.82e+00 angle pdb=" C03 G4C R 503 " pdb=" N04 G4C R 503 " pdb=" C16 G4C R 503 " ideal model delta sigma weight residual 119.52 112.47 7.05 3.00e+00 1.11e-01 5.53e+00 ... (remaining 11265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.78: 4656 21.78 - 43.56: 271 43.56 - 65.34: 38 65.34 - 87.12: 10 87.12 - 108.90: 6 Dihedral angle restraints: 4981 sinusoidal: 1959 harmonic: 3022 Sorted by residual: dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -35.36 -50.64 1 1.00e+01 1.00e-02 3.51e+01 dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 186 " pdb=" CB CYS R 186 " ideal model delta sinusoidal sigma weight residual 93.00 58.75 34.25 1 1.00e+01 1.00e-02 1.66e+01 dihedral pdb=" C02 G4C R 503 " pdb=" C03 G4C R 503 " pdb=" C30 G4C R 503 " pdb=" C19 G4C R 503 " ideal model delta sinusoidal sigma weight residual 66.31 175.21 -108.90 1 3.00e+01 1.11e-03 1.41e+01 ... (remaining 4978 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 796 0.031 - 0.062: 351 0.062 - 0.093: 94 0.093 - 0.124: 37 0.124 - 0.155: 4 Chirality restraints: 1282 Sorted by residual: chirality pdb=" C16 G4C R 503 " pdb=" C17 G4C R 503 " pdb=" C18 G4C R 503 " pdb=" N04 G4C R 503 " both_signs ideal model delta sigma weight residual False -2.47 -2.62 0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CB VAL N 110 " pdb=" CA VAL N 110 " pdb=" CG1 VAL N 110 " pdb=" CG2 VAL N 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA ILE B 232 " pdb=" N ILE B 232 " pdb=" C ILE B 232 " pdb=" CB ILE B 232 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.43e-01 ... (remaining 1279 not shown) Planarity restraints: 1422 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE R 205 " 0.025 5.00e-02 4.00e+02 3.82e-02 2.33e+00 pdb=" N PRO R 206 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO R 206 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO R 206 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.021 5.00e-02 4.00e+02 3.25e-02 1.69e+00 pdb=" N PRO A 332 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO G 49 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " -0.017 5.00e-02 4.00e+02 ... (remaining 1419 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.24: 10 2.24 - 2.90: 3394 2.90 - 3.57: 12658 3.57 - 4.23: 21924 4.23 - 4.90: 35845 Nonbonded interactions: 73831 Sorted by model distance: nonbonded pdb=" OD1 ASN B 119 " pdb=" O GLY B 144 " model vdw 1.570 3.040 nonbonded pdb=" OD1 ASN B 119 " pdb=" C GLY B 144 " model vdw 1.910 3.270 nonbonded pdb=" OG SER R 202 " pdb=" O2 LDP R 502 " model vdw 2.070 2.440 nonbonded pdb=" O ILE R 154 " pdb=" OH TYR R 194 " model vdw 2.149 2.440 nonbonded pdb=" O ALA R 101 " pdb=" OG SER R 155 " model vdw 2.179 2.440 ... (remaining 73826 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: 0.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 2.610 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.880 Find NCS groups from input model: 0.380 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:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6891 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 : 0.003 0.126 8304 Z= 0.206 Angle : 0.519 9.377 11270 Z= 0.296 Chirality : 0.039 0.155 1282 Planarity : 0.003 0.038 1422 Dihedral : 14.328 108.900 3005 Min Nonbonded Distance : 1.570 Molprobity Statistics. All-atom Clashscore : 22.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 0.93 % Allowed : 8.14 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.38 (0.23), residues: 1017 helix: -1.83 (0.21), residues: 396 sheet: -2.71 (0.31), residues: 200 loop : -2.20 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.004 0.001 HIS A 357 PHE 0.009 0.001 PHE R 20 TYR 0.009 0.001 TYR N 117 ARG 0.002 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 270 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5446 (t80) cc_final: 0.4474 (t80) REVERT: A 339 TYR cc_start: 0.8230 (m-80) cc_final: 0.7793 (m-80) REVERT: A 343 ASP cc_start: 0.7415 (m-30) cc_final: 0.7078 (m-30) REVERT: A 386 MET cc_start: 0.7538 (ttp) cc_final: 0.7265 (ttm) REVERT: B 247 ASP cc_start: 0.8084 (p0) cc_final: 0.7806 (p0) REVERT: N 94 TYR cc_start: 0.8186 (m-80) cc_final: 0.7947 (m-80) REVERT: N 95 TYR cc_start: 0.8270 (m-80) cc_final: 0.7959 (m-80) REVERT: R 156 PHE cc_start: 0.6519 (m-10) cc_final: 0.5909 (m-80) REVERT: R 292 ASN cc_start: 0.8348 (t0) cc_final: 0.8064 (t0) outliers start: 8 outliers final: 3 residues processed: 274 average time/residue: 0.2592 time to fit residues: 90.7780 Evaluate side-chains 210 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 207 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.0470 chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.1682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN A 41 HIS ** A 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 278 ASN ** A 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS B 293 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 44 HIS N 13 GLN N 31 ASN N 39 GLN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8304 Z= 0.307 Angle : 0.606 13.181 11270 Z= 0.313 Chirality : 0.044 0.306 1282 Planarity : 0.005 0.044 1422 Dihedral : 6.919 73.307 1215 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.44 % Allowed : 16.16 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.25), residues: 1017 helix: -0.58 (0.24), residues: 397 sheet: -2.69 (0.33), residues: 188 loop : -1.66 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 211 HIS 0.005 0.001 HIS A 362 PHE 0.016 0.002 PHE B 151 TYR 0.016 0.002 TYR B 264 ARG 0.005 0.001 ARG R 192 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 224 time to evaluate : 0.850 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8184 (tppt) cc_final: 0.7682 (mmtm) REVERT: A 222 PHE cc_start: 0.5525 (t80) cc_final: 0.4649 (t80) REVERT: A 291 LEU cc_start: 0.8189 (mt) cc_final: 0.7667 (mt) REVERT: A 318 TYR cc_start: 0.7536 (t80) cc_final: 0.7260 (t80) REVERT: A 339 TYR cc_start: 0.8410 (m-80) cc_final: 0.7759 (m-80) REVERT: A 343 ASP cc_start: 0.7508 (m-30) cc_final: 0.7222 (m-30) REVERT: A 386 MET cc_start: 0.7467 (ttp) cc_final: 0.7224 (ttm) REVERT: B 87 THR cc_start: 0.7321 (m) cc_final: 0.6963 (m) REVERT: B 124 TYR cc_start: 0.8883 (m-80) cc_final: 0.8531 (m-80) REVERT: B 228 ASP cc_start: 0.7053 (OUTLIER) cc_final: 0.6796 (m-30) REVERT: B 247 ASP cc_start: 0.8157 (p0) cc_final: 0.7870 (p0) REVERT: B 262 MET cc_start: 0.7758 (tpp) cc_final: 0.7475 (tpp) REVERT: B 289 TYR cc_start: 0.8544 (m-80) cc_final: 0.8341 (m-80) REVERT: B 323 ASP cc_start: 0.7243 (p0) cc_final: 0.6684 (p0) REVERT: G 29 LYS cc_start: 0.8564 (mmtm) cc_final: 0.8282 (mmtm) REVERT: R 156 PHE cc_start: 0.7022 (m-10) cc_final: 0.6758 (m-10) REVERT: R 319 PHE cc_start: 0.7920 (OUTLIER) cc_final: 0.7286 (t80) outliers start: 21 outliers final: 12 residues processed: 236 average time/residue: 0.2217 time to fit residues: 69.9491 Evaluate side-chains 212 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 198 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 319 PHE Chi-restraints excluded: chain R residue 325 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 0.0980 chunk 25 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 99 optimal weight: 0.6980 chunk 81 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN R 323 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8304 Z= 0.197 Angle : 0.523 8.671 11270 Z= 0.273 Chirality : 0.041 0.155 1282 Planarity : 0.004 0.044 1422 Dihedral : 4.959 54.043 1215 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 19.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.84 % Allowed : 18.02 % Favored : 78.14 % 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: -1.73 (0.26), residues: 1017 helix: -0.11 (0.25), residues: 394 sheet: -2.39 (0.35), residues: 192 loop : -1.38 (0.30), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.007 0.001 HIS A 41 PHE 0.017 0.001 PHE B 151 TYR 0.012 0.001 TYR B 264 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 216 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8120 (tppt) cc_final: 0.7604 (mmtm) REVERT: A 222 PHE cc_start: 0.5256 (t80) cc_final: 0.4473 (t80) REVERT: A 294 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7377 (mm-40) REVERT: A 318 TYR cc_start: 0.7308 (t80) cc_final: 0.7077 (t80) REVERT: A 343 ASP cc_start: 0.7478 (m-30) cc_final: 0.7209 (m-30) REVERT: B 124 TYR cc_start: 0.8835 (m-80) cc_final: 0.8631 (m-80) REVERT: B 228 ASP cc_start: 0.6783 (OUTLIER) cc_final: 0.6562 (m-30) REVERT: B 247 ASP cc_start: 0.8079 (p0) cc_final: 0.7762 (p0) REVERT: B 289 TYR cc_start: 0.8472 (m-80) cc_final: 0.8263 (m-80) REVERT: G 29 LYS cc_start: 0.8556 (mmtm) cc_final: 0.8332 (tppt) REVERT: N 80 TYR cc_start: 0.8337 (m-80) cc_final: 0.8078 (m-80) REVERT: R 142 ILE cc_start: 0.7408 (mt) cc_final: 0.7136 (mt) REVERT: R 154 ILE cc_start: 0.8394 (mm) cc_final: 0.8126 (mt) REVERT: R 319 PHE cc_start: 0.7821 (OUTLIER) cc_final: 0.7251 (t80) outliers start: 33 outliers final: 22 residues processed: 235 average time/residue: 0.2235 time to fit residues: 69.9493 Evaluate side-chains 222 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 196 ILE Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 295 LEU Chi-restraints excluded: chain R residue 319 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 97 optimal weight: 8.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 0.3980 chunk 81 optimal weight: 0.0020 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 236 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8304 Z= 0.247 Angle : 0.541 7.600 11270 Z= 0.278 Chirality : 0.041 0.139 1282 Planarity : 0.004 0.046 1422 Dihedral : 4.907 54.758 1214 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 3.72 % Allowed : 20.23 % Favored : 76.05 % 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: -1.62 (0.26), residues: 1017 helix: -0.06 (0.25), residues: 401 sheet: -2.26 (0.35), residues: 193 loop : -1.32 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 123 HIS 0.006 0.001 HIS A 41 PHE 0.017 0.002 PHE B 151 TYR 0.020 0.002 TYR B 264 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 202 time to evaluate : 0.901 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8229 (tppt) cc_final: 0.7662 (mmtm) REVERT: A 222 PHE cc_start: 0.5303 (t80) cc_final: 0.5066 (t80) REVERT: A 291 LEU cc_start: 0.8051 (mt) cc_final: 0.7680 (mp) REVERT: A 343 ASP cc_start: 0.7437 (m-30) cc_final: 0.7216 (m-30) REVERT: B 124 TYR cc_start: 0.8905 (m-80) cc_final: 0.8694 (m-80) REVERT: B 228 ASP cc_start: 0.6995 (OUTLIER) cc_final: 0.6730 (m-30) REVERT: B 289 TYR cc_start: 0.8600 (m-80) cc_final: 0.8281 (m-80) REVERT: B 297 TRP cc_start: 0.8888 (m100) cc_final: 0.8523 (m100) REVERT: R 142 ILE cc_start: 0.7606 (mt) cc_final: 0.7288 (mt) REVERT: R 154 ILE cc_start: 0.8428 (mm) cc_final: 0.8174 (mt) REVERT: R 210 MET cc_start: 0.7790 (ttm) cc_final: 0.7572 (ttm) outliers start: 32 outliers final: 23 residues processed: 220 average time/residue: 0.2084 time to fit residues: 61.3692 Evaluate side-chains 211 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 187 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 292 ASN Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 202 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 0.0000 chunk 40 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 29 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 371 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN N 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8304 Z= 0.195 Angle : 0.507 7.414 11270 Z= 0.267 Chirality : 0.041 0.137 1282 Planarity : 0.004 0.057 1422 Dihedral : 4.817 56.216 1214 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 18.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.19 % Allowed : 20.12 % Favored : 75.70 % 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: -1.35 (0.26), residues: 1017 helix: 0.18 (0.26), residues: 395 sheet: -2.27 (0.34), residues: 209 loop : -1.02 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.016 0.001 PHE B 151 TYR 0.016 0.001 TYR R 214 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8214 (tppt) cc_final: 0.7701 (mmtm) REVERT: A 208 PHE cc_start: 0.4377 (OUTLIER) cc_final: 0.3769 (t80) REVERT: A 222 PHE cc_start: 0.5442 (t80) cc_final: 0.5101 (t80) REVERT: A 291 LEU cc_start: 0.8129 (mt) cc_final: 0.7847 (mp) REVERT: A 338 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.7832 (ttmt) REVERT: B 209 LYS cc_start: 0.8741 (mttp) cc_final: 0.8529 (mttp) REVERT: B 228 ASP cc_start: 0.6921 (OUTLIER) cc_final: 0.6670 (m-30) REVERT: B 289 TYR cc_start: 0.8567 (m-80) cc_final: 0.8274 (m-80) REVERT: B 297 TRP cc_start: 0.8872 (m100) cc_final: 0.8544 (m100) REVERT: B 323 ASP cc_start: 0.7665 (p0) cc_final: 0.7273 (p0) REVERT: G 29 LYS cc_start: 0.8626 (tptm) cc_final: 0.8372 (tppt) REVERT: N 80 TYR cc_start: 0.8285 (m-80) cc_final: 0.7983 (m-80) REVERT: R 142 ILE cc_start: 0.7613 (mt) cc_final: 0.7279 (mt) REVERT: R 154 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8200 (mt) REVERT: R 163 TRP cc_start: 0.6105 (m100) cc_final: 0.5659 (m100) REVERT: R 319 PHE cc_start: 0.7737 (OUTLIER) cc_final: 0.7147 (t80) outliers start: 36 outliers final: 24 residues processed: 219 average time/residue: 0.2063 time to fit residues: 60.7629 Evaluate side-chains 217 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 PHE Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 151 PHE Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 202 SER Chi-restraints excluded: chain R residue 319 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 0.0870 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 overall best weight: 1.3562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 29 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 377 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 8304 Z= 0.340 Angle : 0.576 7.146 11270 Z= 0.300 Chirality : 0.043 0.170 1282 Planarity : 0.004 0.048 1422 Dihedral : 5.125 56.717 1214 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 22.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.53 % Allowed : 21.86 % Favored : 73.60 % 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: -1.42 (0.26), residues: 1017 helix: 0.06 (0.25), residues: 400 sheet: -2.26 (0.34), residues: 205 loop : -1.06 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.008 0.001 HIS A 41 PHE 0.019 0.002 PHE B 151 TYR 0.019 0.002 TYR B 264 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 197 time to evaluate : 0.919 Fit side-chains REVERT: A 17 LYS cc_start: 0.8171 (tppt) cc_final: 0.7671 (mmtm) REVERT: A 31 GLN cc_start: 0.7644 (mm-40) cc_final: 0.7391 (mm110) REVERT: A 222 PHE cc_start: 0.5811 (t80) cc_final: 0.5434 (t80) REVERT: A 338 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8290 (ttmt) REVERT: B 124 TYR cc_start: 0.9001 (m-80) cc_final: 0.8730 (m-80) REVERT: B 228 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6962 (m-30) REVERT: B 289 TYR cc_start: 0.8747 (m-80) cc_final: 0.8361 (m-80) REVERT: B 297 TRP cc_start: 0.8911 (m100) cc_final: 0.8567 (m100) REVERT: B 323 ASP cc_start: 0.7777 (p0) cc_final: 0.7434 (p0) REVERT: G 29 LYS cc_start: 0.8584 (tptm) cc_final: 0.8332 (tppt) REVERT: R 142 ILE cc_start: 0.7691 (mt) cc_final: 0.7351 (mt) REVERT: R 154 ILE cc_start: 0.8476 (OUTLIER) cc_final: 0.8212 (mt) outliers start: 39 outliers final: 27 residues processed: 218 average time/residue: 0.2126 time to fit residues: 61.9138 Evaluate side-chains 217 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 187 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 154 ILE Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 71 optimal weight: 4.9990 chunk 82 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN A 390 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8304 Z= 0.245 Angle : 0.542 7.369 11270 Z= 0.284 Chirality : 0.042 0.149 1282 Planarity : 0.004 0.049 1422 Dihedral : 5.052 59.744 1214 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 21.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 4.19 % Allowed : 21.74 % Favored : 74.07 % 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: -1.32 (0.26), residues: 1017 helix: 0.17 (0.26), residues: 398 sheet: -2.20 (0.34), residues: 204 loop : -1.02 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.018 0.001 PHE A 376 TYR 0.015 0.002 TYR B 264 ARG 0.005 0.000 ARG A 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 192 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8209 (tppt) cc_final: 0.7731 (mmtm) REVERT: A 208 PHE cc_start: 0.4168 (t80) cc_final: 0.3361 (t80) REVERT: A 222 PHE cc_start: 0.5425 (t80) cc_final: 0.5096 (t80) REVERT: A 255 MET cc_start: -0.0059 (mmp) cc_final: -0.1258 (mtp) REVERT: A 263 THR cc_start: 0.6457 (m) cc_final: 0.5647 (t) REVERT: A 338 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8361 (ttmt) REVERT: B 124 TYR cc_start: 0.8934 (m-80) cc_final: 0.8682 (m-80) REVERT: B 209 LYS cc_start: 0.8645 (mttp) cc_final: 0.8395 (mmtm) REVERT: B 228 ASP cc_start: 0.7010 (OUTLIER) cc_final: 0.6785 (m-30) REVERT: B 289 TYR cc_start: 0.8691 (m-80) cc_final: 0.8308 (m-80) REVERT: B 297 TRP cc_start: 0.8886 (m100) cc_final: 0.8554 (m100) REVERT: B 323 ASP cc_start: 0.7694 (p0) cc_final: 0.7305 (p0) REVERT: B 329 THR cc_start: 0.8789 (m) cc_final: 0.8419 (p) REVERT: G 29 LYS cc_start: 0.8598 (tptm) cc_final: 0.8336 (tppt) REVERT: R 142 ILE cc_start: 0.7716 (mt) cc_final: 0.7389 (mt) REVERT: R 154 ILE cc_start: 0.8375 (mm) cc_final: 0.8057 (mt) outliers start: 36 outliers final: 28 residues processed: 212 average time/residue: 0.2382 time to fit residues: 68.6273 Evaluate side-chains 210 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 180 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 9.9990 chunk 93 optimal weight: 0.8980 chunk 85 optimal weight: 0.0970 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8304 Z= 0.206 Angle : 0.535 9.740 11270 Z= 0.278 Chirality : 0.041 0.149 1282 Planarity : 0.004 0.049 1422 Dihedral : 4.968 59.497 1214 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.53 % Allowed : 21.86 % Favored : 73.60 % 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: -1.12 (0.27), residues: 1017 helix: 0.35 (0.26), residues: 394 sheet: -2.20 (0.34), residues: 205 loop : -0.85 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 234 HIS 0.006 0.001 HIS A 41 PHE 0.016 0.001 PHE B 151 TYR 0.013 0.001 TYR B 264 ARG 0.004 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8246 (tppt) cc_final: 0.7694 (mmtm) REVERT: A 208 PHE cc_start: 0.3746 (t80) cc_final: 0.2938 (t80) REVERT: A 222 PHE cc_start: 0.5384 (t80) cc_final: 0.5015 (t80) REVERT: A 255 MET cc_start: -0.0147 (mmp) cc_final: -0.1290 (mtp) REVERT: A 263 THR cc_start: 0.6265 (OUTLIER) cc_final: 0.5543 (t) REVERT: A 338 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8307 (ttmt) REVERT: A 381 ASP cc_start: 0.7694 (m-30) cc_final: 0.7264 (t0) REVERT: B 124 TYR cc_start: 0.8887 (m-80) cc_final: 0.8627 (m-80) REVERT: B 197 ARG cc_start: 0.7375 (tpp80) cc_final: 0.6909 (tpp80) REVERT: B 209 LYS cc_start: 0.8615 (mttp) cc_final: 0.8363 (mmtm) REVERT: B 228 ASP cc_start: 0.6929 (OUTLIER) cc_final: 0.6699 (m-30) REVERT: B 289 TYR cc_start: 0.8656 (m-80) cc_final: 0.8293 (m-80) REVERT: B 297 TRP cc_start: 0.8826 (m100) cc_final: 0.8480 (m100) REVERT: B 323 ASP cc_start: 0.7591 (p0) cc_final: 0.7181 (p0) REVERT: B 329 THR cc_start: 0.8794 (m) cc_final: 0.8432 (p) REVERT: G 29 LYS cc_start: 0.8620 (tptm) cc_final: 0.8383 (tppt) REVERT: N 80 TYR cc_start: 0.8299 (m-80) cc_final: 0.8052 (m-80) REVERT: R 142 ILE cc_start: 0.7632 (mt) cc_final: 0.7311 (mt) REVERT: R 154 ILE cc_start: 0.8407 (mm) cc_final: 0.8079 (mt) outliers start: 39 outliers final: 30 residues processed: 214 average time/residue: 0.2192 time to fit residues: 62.3553 Evaluate side-chains 220 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 187 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 202 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 0.9980 chunk 93 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8304 Z= 0.258 Angle : 0.558 9.530 11270 Z= 0.288 Chirality : 0.042 0.161 1282 Planarity : 0.004 0.052 1422 Dihedral : 4.977 59.287 1214 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 20.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 4.53 % Allowed : 22.79 % Favored : 72.67 % 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: -1.09 (0.27), residues: 1017 helix: 0.37 (0.26), residues: 398 sheet: -2.11 (0.33), residues: 215 loop : -0.83 (0.33), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 63 HIS 0.006 0.001 HIS A 41 PHE 0.015 0.001 PHE A 376 TYR 0.013 0.001 TYR B 264 ARG 0.006 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 188 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8245 (tppt) cc_final: 0.7729 (mmtm) REVERT: A 208 PHE cc_start: 0.3876 (t80) cc_final: 0.3159 (t80) REVERT: A 222 PHE cc_start: 0.5521 (t80) cc_final: 0.5102 (t80) REVERT: A 255 MET cc_start: -0.0056 (mmp) cc_final: -0.1393 (mtp) REVERT: A 263 THR cc_start: 0.6331 (OUTLIER) cc_final: 0.5572 (t) REVERT: A 338 LYS cc_start: 0.8709 (OUTLIER) cc_final: 0.8312 (ttmt) REVERT: A 381 ASP cc_start: 0.7717 (m-30) cc_final: 0.7281 (t0) REVERT: B 124 TYR cc_start: 0.8946 (m-80) cc_final: 0.8696 (m-80) REVERT: B 197 ARG cc_start: 0.7435 (tpp80) cc_final: 0.6971 (tpp80) REVERT: B 209 LYS cc_start: 0.8642 (mttp) cc_final: 0.8387 (mmtm) REVERT: B 228 ASP cc_start: 0.7008 (OUTLIER) cc_final: 0.6783 (m-30) REVERT: B 289 TYR cc_start: 0.8726 (m-80) cc_final: 0.8373 (m-80) REVERT: B 297 TRP cc_start: 0.8851 (m100) cc_final: 0.8508 (m100) REVERT: B 323 ASP cc_start: 0.7643 (p0) cc_final: 0.7204 (p0) REVERT: B 329 THR cc_start: 0.8843 (m) cc_final: 0.8478 (p) REVERT: G 29 LYS cc_start: 0.8643 (tptm) cc_final: 0.8381 (tppt) REVERT: N 80 TYR cc_start: 0.8299 (m-80) cc_final: 0.8047 (m-80) REVERT: R 142 ILE cc_start: 0.7689 (mt) cc_final: 0.7371 (mt) REVERT: R 154 ILE cc_start: 0.8427 (mm) cc_final: 0.8108 (mt) outliers start: 39 outliers final: 31 residues processed: 211 average time/residue: 0.2133 time to fit residues: 60.1812 Evaluate side-chains 220 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 186 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 0.2980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7203 moved from start: 0.4278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8304 Z= 0.235 Angle : 0.554 9.783 11270 Z= 0.286 Chirality : 0.042 0.157 1282 Planarity : 0.004 0.049 1422 Dihedral : 4.942 58.126 1214 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 4.30 % Allowed : 23.49 % Favored : 72.21 % 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: 1017 helix: 0.44 (0.26), residues: 398 sheet: -2.04 (0.34), residues: 214 loop : -0.75 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 63 HIS 0.005 0.001 HIS A 41 PHE 0.018 0.001 PHE A 376 TYR 0.013 0.002 TYR B 264 ARG 0.005 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 188 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 222 PHE cc_start: 0.5541 (t80) cc_final: 0.5295 (t80) REVERT: A 255 MET cc_start: -0.0104 (mmp) cc_final: -0.1420 (mtp) REVERT: A 263 THR cc_start: 0.6352 (OUTLIER) cc_final: 0.5615 (t) REVERT: A 338 LYS cc_start: 0.8735 (OUTLIER) cc_final: 0.8277 (ttmt) REVERT: A 381 ASP cc_start: 0.7724 (m-30) cc_final: 0.7286 (t0) REVERT: B 124 TYR cc_start: 0.8963 (m-80) cc_final: 0.8742 (m-80) REVERT: B 197 ARG cc_start: 0.7370 (tpp80) cc_final: 0.6955 (tpp80) REVERT: B 209 LYS cc_start: 0.8616 (mttp) cc_final: 0.8376 (mmtm) REVERT: B 228 ASP cc_start: 0.6980 (OUTLIER) cc_final: 0.6756 (m-30) REVERT: B 289 TYR cc_start: 0.8694 (m-80) cc_final: 0.8232 (m-80) REVERT: B 297 TRP cc_start: 0.8837 (m100) cc_final: 0.8492 (m100) REVERT: B 323 ASP cc_start: 0.7699 (p0) cc_final: 0.7310 (p0) REVERT: B 329 THR cc_start: 0.8811 (m) cc_final: 0.8460 (p) REVERT: G 29 LYS cc_start: 0.8644 (tptm) cc_final: 0.8382 (tppt) REVERT: N 80 TYR cc_start: 0.8268 (m-80) cc_final: 0.8050 (m-80) REVERT: R 142 ILE cc_start: 0.7705 (mt) cc_final: 0.7391 (mt) REVERT: R 154 ILE cc_start: 0.8385 (mm) cc_final: 0.8068 (mt) outliers start: 37 outliers final: 33 residues processed: 211 average time/residue: 0.2137 time to fit residues: 60.1222 Evaluate side-chains 218 residues out of total 892 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 182 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 209 GLU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 229 ASP Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 371 ASN Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 157 ILE Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 52 SER Chi-restraints excluded: chain N residue 64 VAL Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 117 TYR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain R residue 59 THR Chi-restraints excluded: chain R residue 60 ASN Chi-restraints excluded: chain R residue 102 PHE Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 150 LEU Chi-restraints excluded: chain R residue 190 LEU Chi-restraints excluded: chain R residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 80 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.180256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.145805 restraints weight = 9192.044| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.06 r_work: 0.3534 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8304 Z= 0.245 Angle : 0.558 12.778 11270 Z= 0.287 Chirality : 0.042 0.157 1282 Planarity : 0.004 0.049 1422 Dihedral : 4.933 58.087 1214 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.07 % Allowed : 23.60 % Favored : 72.33 % 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: -0.95 (0.27), residues: 1017 helix: 0.46 (0.26), residues: 398 sheet: -2.04 (0.34), residues: 214 loop : -0.73 (0.33), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 99 HIS 0.005 0.001 HIS A 41 PHE 0.017 0.002 PHE A 376 TYR 0.013 0.002 TYR B 264 ARG 0.006 0.000 ARG A 333 =============================================================================== Job complete usr+sys time: 2337.41 seconds wall clock time: 43 minutes 0.05 seconds (2580.05 seconds total)