Starting phenix.real_space_refine on Wed Feb 14 10:42:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vcb_21147/02_2024/6vcb_21147_neut_updated.pdb" } resolution = 3.3 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= 0.004 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: 5 Type Number sf(0) Gaussians S 54 5.16 5 Cl 2 4.86 5 C 5787 2.51 5 N 1573 2.21 5 O 1658 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R TYR 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 326": "NH1" <-> "NH2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R ARG 380": "NH1" <-> "NH2" Residue "R ARG 414": "NH1" <-> "NH2" Residue "A ARG 374": "NH1" <-> "NH2" Residue "A ARG 380": "NH1" <-> "NH2" Residue "B ARG 46": "NH1" <-> "NH2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 314": "NH1" <-> "NH2" Residue "N PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 98": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9074 Number of models: 1 Model: "" Number of chains: 7 Chain: "R" Number of atoms: 3000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3000 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PTRANS': 14, 'TRANS': 363} Chain breaks: 3 Unresolved non-hydrogen bonds: 143 Unresolved non-hydrogen angles: 186 Unresolved non-hydrogen dihedrals: 118 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 5, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "P" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 231 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 30} 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: "A" Number of atoms: 1810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1810 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 6, 'TRANS': 216} Chain breaks: 5 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2581 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2581 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "G" Number of atoms: 453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 453 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 4, 'TRANS': 54} Chain: "N" Number of atoms: 966 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 966 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 33 Unusual residues: {'QW7': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.95, per 1000 atoms: 0.66 Number of scatterers: 9074 At special positions: 0 Unit cell: (166.4, 102.96, 98.8, 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 54 16.00 O 1658 8.00 N 1573 7.00 C 5787 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.03 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.02 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: 3.59 Conformation dependent library (CDL) restraints added in 2.0 seconds 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2180 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 11 sheets defined 37.3% alpha, 17.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.75 Creating SS restraints... Processing helix chain 'R' and resid 32 through 50 Processing helix chain 'R' and resid 90 through 92 No H-bonds generated for 'chain 'R' and resid 90 through 92' Processing helix chain 'R' and resid 138 through 167 removed outlier: 3.681A pdb=" N LEU R 142 " --> pdb=" O GLU R 138 " (cutoff:3.500A) Processing helix chain 'R' and resid 175 through 205 Processing helix chain 'R' and resid 217 through 222 removed outlier: 3.898A pdb=" N ASP R 222 " --> pdb=" O LEU R 218 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 255 Processing helix chain 'R' and resid 262 through 273 removed outlier: 3.638A pdb=" N ARG R 267 " --> pdb=" O GLN R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 276 through 290 Proline residue: R 283 - end of helix Processing helix chain 'R' and resid 304 through 335 removed outlier: 4.504A pdb=" N ILE R 309 " --> pdb=" O TYR R 305 " (cutoff:3.500A) Proline residue: R 312 - end of helix Processing helix chain 'R' and resid 346 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 363 through 367 Processing helix chain 'R' and resid 378 through 401 removed outlier: 4.100A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 420 Processing helix chain 'P' and resid 9 through 33 Processing helix chain 'A' and resid 11 through 37 Processing helix chain 'A' and resid 53 through 57 removed outlier: 3.974A pdb=" N VAL A 57 " --> pdb=" O SER A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 237 No H-bonds generated for 'chain 'A' and resid 235 through 237' Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 294 through 301 Processing helix chain 'A' and resid 308 through 311 No H-bonds generated for 'chain 'A' and resid 308 through 311' Processing helix chain 'A' and resid 314 through 316 No H-bonds generated for 'chain 'A' and resid 314 through 316' Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'A' and resid 371 through 390 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 33 No H-bonds generated for 'chain 'B' and resid 30 through 33' Processing helix chain 'G' and resid 6 through 23 removed outlier: 4.116A pdb=" N ALA G 10 " --> pdb=" O THR G 6 " (cutoff:3.500A) removed outlier: 3.875A 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 62 through 64 No H-bonds generated for 'chain 'N' and resid 62 through 64' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'R' and resid 79 through 84 Processing sheet with id= B, first strand: chain 'A' and resid 359 through 361 removed outlier: 7.098A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 50 through 52 removed outlier: 3.527A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.040A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.741A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.803A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.129A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 220 through 222 Processing sheet with id= H, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.956A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N THR B 249 " --> pdb=" O SER B 245 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 275 through 278 removed outlier: 6.259A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (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 122 through 124 removed outlier: 5.854A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1218 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: 2.64 Time building geometry restraints manager: 3.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2908 1.34 - 1.46: 2128 1.46 - 1.58: 4167 1.58 - 1.70: 0 1.70 - 1.82: 74 Bond restraints: 9277 Sorted by residual: bond pdb=" C17 QW7 R 501 " pdb=" C18 QW7 R 501 " ideal model delta sigma weight residual 1.528 1.391 0.137 2.00e-02 2.50e+03 4.67e+01 bond pdb=" CG LEU R 159 " pdb=" CD1 LEU R 159 " ideal model delta sigma weight residual 1.521 1.427 0.094 3.30e-02 9.18e+02 8.06e+00 bond pdb=" CG LEU R 159 " pdb=" CD2 LEU R 159 " ideal model delta sigma weight residual 1.521 1.447 0.074 3.30e-02 9.18e+02 5.08e+00 bond pdb=" C TRP R 214 " pdb=" N ASP R 215 " ideal model delta sigma weight residual 1.333 1.301 0.032 1.51e-02 4.39e+03 4.55e+00 bond pdb=" CB GLU R 247 " pdb=" CG GLU R 247 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.06e+00 ... (remaining 9272 not shown) Histogram of bond angle deviations from ideal: 95.90 - 103.63: 83 103.63 - 111.36: 3630 111.36 - 119.09: 3825 119.09 - 126.82: 4904 126.82 - 134.55: 151 Bond angle restraints: 12593 Sorted by residual: angle pdb=" C03 QW7 R 501 " pdb=" C32 QW7 R 501 " pdb="CL33 QW7 R 501 " ideal model delta sigma weight residual 92.03 119.99 -27.96 3.00e+00 1.11e-01 8.69e+01 angle pdb=" C08 QW7 R 501 " pdb=" C32 QW7 R 501 " pdb="CL33 QW7 R 501 " ideal model delta sigma weight residual 146.30 120.08 26.22 3.00e+00 1.11e-01 7.64e+01 angle pdb=" C09 QW7 R 501 " pdb=" N11 QW7 R 501 " pdb=" C12 QW7 R 501 " ideal model delta sigma weight residual 103.26 125.89 -22.63 3.00e+00 1.11e-01 5.69e+01 angle pdb=" C09 QW7 R 501 " pdb=" N11 QW7 R 501 " pdb=" C31 QW7 R 501 " ideal model delta sigma weight residual 147.39 125.90 21.49 3.00e+00 1.11e-01 5.13e+01 angle pdb=" CA LEU A 46 " pdb=" CB LEU A 46 " pdb=" CG LEU A 46 " ideal model delta sigma weight residual 116.30 134.55 -18.25 3.50e+00 8.16e-02 2.72e+01 ... (remaining 12588 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.74: 5054 15.74 - 31.48: 312 31.48 - 47.21: 75 47.21 - 62.95: 10 62.95 - 78.69: 10 Dihedral angle restraints: 5461 sinusoidal: 2094 harmonic: 3367 Sorted by residual: dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -152.86 66.86 1 1.00e+01 1.00e-02 5.83e+01 dihedral pdb=" CB CYS R 226 " pdb=" SG CYS R 226 " pdb=" SG CYS R 296 " pdb=" CB CYS R 296 " ideal model delta sinusoidal sigma weight residual 93.00 145.59 -52.59 1 1.00e+01 1.00e-02 3.77e+01 dihedral pdb=" CA CYS N 99 " pdb=" C CYS N 99 " pdb=" N PRO N 100 " pdb=" CA PRO N 100 " ideal model delta harmonic sigma weight residual -180.00 -155.02 -24.98 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 5458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 1022 0.060 - 0.121: 319 0.121 - 0.181: 48 0.181 - 0.242: 10 0.242 - 0.302: 5 Chirality restraints: 1404 Sorted by residual: chirality pdb=" CG LEU A 44 " pdb=" CB LEU A 44 " pdb=" CD1 LEU A 44 " pdb=" CD2 LEU A 44 " both_signs ideal model delta sigma weight residual False -2.59 -2.29 -0.30 2.00e-01 2.50e+01 2.28e+00 chirality pdb=" CG LEU R 183 " pdb=" CB LEU R 183 " pdb=" CD1 LEU R 183 " pdb=" CD2 LEU R 183 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 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 -2.36 -0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 1401 not shown) Planarity restraints: 1599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR R 242 " -0.018 2.00e-02 2.50e+03 1.75e-02 6.10e+00 pdb=" CG TYR R 242 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR R 242 " -0.017 2.00e-02 2.50e+03 pdb=" CD2 TYR R 242 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR R 242 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR R 242 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR R 242 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 169 " 0.021 2.00e-02 2.50e+03 1.50e-02 5.63e+00 pdb=" CG TRP B 169 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP B 169 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 169 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 169 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 169 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 169 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 282 " -0.039 5.00e-02 4.00e+02 5.82e-02 5.42e+00 pdb=" N PRO R 283 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 283 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 283 " -0.033 5.00e-02 4.00e+02 ... (remaining 1596 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 197 2.67 - 3.23: 8349 3.23 - 3.79: 14911 3.79 - 4.34: 19408 4.34 - 4.90: 31846 Nonbonded interactions: 74711 Sorted by model distance: nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.117 2.440 nonbonded pdb=" OD2 ASP B 212 " pdb=" NH2 ARG B 219 " model vdw 2.145 2.520 nonbonded pdb=" OE2 GLU N 6 " pdb=" N GLY N 121 " model vdw 2.159 2.520 nonbonded pdb=" NE2 HIS A 362 " pdb=" OD2 ASP A 378 " model vdw 2.160 2.520 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.222 2.440 ... (remaining 74706 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: 0.010 Normalize map: mean=0, sd=1: 0.950 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: 0.020 Extract box with map and model: 3.500 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 30.010 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 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 0.137 9277 Z= 0.421 Angle : 1.091 27.959 12593 Z= 0.550 Chirality : 0.060 0.302 1404 Planarity : 0.007 0.058 1599 Dihedral : 11.630 78.687 3263 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.85 % Allowed : 5.32 % Favored : 93.82 % 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: -4.29 (0.19), residues: 1130 helix: -2.61 (0.17), residues: 456 sheet: -2.38 (0.30), residues: 218 loop : -3.17 (0.22), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP B 169 HIS 0.010 0.002 HIS B 142 PHE 0.021 0.003 PHE R 280 TYR 0.041 0.004 TYR R 242 ARG 0.010 0.001 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 267 time to evaluate : 1.106 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7641 (tp30) cc_final: 0.7356 (mt-10) REVERT: R 304 ASN cc_start: 0.7541 (m-40) cc_final: 0.6142 (t0) REVERT: R 372 ASP cc_start: 0.8600 (m-30) cc_final: 0.7942 (m-30) REVERT: R 417 TRP cc_start: 0.6373 (t-100) cc_final: 0.6064 (t-100) REVERT: P 18 SER cc_start: 0.8125 (m) cc_final: 0.7827 (p) REVERT: P 27 GLU cc_start: 0.7702 (tt0) cc_final: 0.7387 (tt0) REVERT: A 338 LYS cc_start: 0.8594 (ttpm) cc_final: 0.8278 (ttpp) REVERT: B 211 TRP cc_start: 0.8795 (m100) cc_final: 0.8570 (m100) REVERT: B 335 PHE cc_start: 0.7892 (m-80) cc_final: 0.7673 (m-10) REVERT: G 19 LEU cc_start: 0.8822 (mt) cc_final: 0.8493 (mt) REVERT: G 46 LYS cc_start: 0.8561 (mppt) cc_final: 0.8351 (mmtm) REVERT: G 48 ASP cc_start: 0.8561 (t70) cc_final: 0.8201 (t0) REVERT: N 82 GLN cc_start: 0.7274 (tp-100) cc_final: 0.7039 (tp-100) REVERT: N 105 ARG cc_start: 0.6366 (mtp-110) cc_final: 0.6160 (mtp-110) outliers start: 8 outliers final: 4 residues processed: 274 average time/residue: 0.2705 time to fit residues: 95.9013 Evaluate side-chains 171 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 167 time to evaluate : 1.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain A residue 43 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 84 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 57 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 8.9990 chunk 101 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN R 210 GLN R 234 GLN R 240 ASN R 374 HIS A 14 ASN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN A 271 ASN A 357 HIS B 266 HIS N 5 GLN N 120 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9277 Z= 0.205 Angle : 0.645 12.386 12593 Z= 0.332 Chirality : 0.044 0.168 1404 Planarity : 0.004 0.040 1599 Dihedral : 6.739 87.035 1274 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 3.83 % Allowed : 11.82 % Favored : 84.35 % 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: -2.91 (0.22), residues: 1130 helix: -0.94 (0.22), residues: 474 sheet: -2.24 (0.31), residues: 201 loop : -2.78 (0.24), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP R 297 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.002 PHE R 280 TYR 0.019 0.002 TYR R 88 ARG 0.006 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 198 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7680 (tp30) cc_final: 0.7331 (mt-10) REVERT: R 279 LEU cc_start: 0.8608 (tt) cc_final: 0.8393 (tt) REVERT: R 299 ARG cc_start: 0.7928 (mmm-85) cc_final: 0.7647 (mmm160) REVERT: R 304 ASN cc_start: 0.7330 (m-40) cc_final: 0.6023 (t0) REVERT: R 373 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7767 (mp0) REVERT: B 10 GLU cc_start: 0.8579 (tm-30) cc_final: 0.8230 (tm-30) REVERT: B 14 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.7449 (tt) REVERT: B 211 TRP cc_start: 0.8815 (m100) cc_final: 0.8582 (m100) REVERT: B 334 SER cc_start: 0.8600 (m) cc_final: 0.8165 (t) REVERT: G 46 LYS cc_start: 0.8596 (mppt) cc_final: 0.8343 (mmtm) REVERT: G 48 ASP cc_start: 0.8403 (t70) cc_final: 0.8072 (t0) REVERT: N 82 GLN cc_start: 0.7396 (tp-100) cc_final: 0.7089 (tp-100) REVERT: N 83 MET cc_start: 0.6911 (mtt) cc_final: 0.6524 (mtt) outliers start: 36 outliers final: 23 residues processed: 223 average time/residue: 0.2251 time to fit residues: 67.5274 Evaluate side-chains 201 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 176 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 84 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 101 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 210 GLN ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN B 155 ASN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9277 Z= 0.206 Angle : 0.611 9.726 12593 Z= 0.313 Chirality : 0.043 0.206 1404 Planarity : 0.004 0.040 1599 Dihedral : 6.428 87.406 1274 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 4.15 % Allowed : 13.63 % Favored : 82.22 % 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: -2.12 (0.23), residues: 1130 helix: -0.10 (0.23), residues: 473 sheet: -2.03 (0.32), residues: 209 loop : -2.45 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 297 HIS 0.005 0.001 HIS B 142 PHE 0.028 0.002 PHE B 199 TYR 0.015 0.002 TYR R 88 ARG 0.005 0.000 ARG R 310 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 192 time to evaluate : 1.018 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7592 (tp30) cc_final: 0.7292 (mt-10) REVERT: R 292 GLU cc_start: 0.7611 (tt0) cc_final: 0.7362 (tt0) REVERT: R 304 ASN cc_start: 0.7403 (m-40) cc_final: 0.6091 (t0) REVERT: R 369 PHE cc_start: 0.4516 (t80) cc_final: 0.3540 (t80) REVERT: A 270 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8758 (mp) REVERT: A 338 LYS cc_start: 0.8522 (ttpm) cc_final: 0.8189 (ttpp) REVERT: B 10 GLU cc_start: 0.8592 (tm-30) cc_final: 0.8122 (tm-30) REVERT: B 280 LYS cc_start: 0.8252 (tttp) cc_final: 0.7952 (tptp) REVERT: G 19 LEU cc_start: 0.8656 (mt) cc_final: 0.8417 (mt) REVERT: G 48 ASP cc_start: 0.8453 (t70) cc_final: 0.7937 (t0) REVERT: N 118 ARG cc_start: 0.8601 (mtm-85) cc_final: 0.8340 (mtm-85) outliers start: 39 outliers final: 29 residues processed: 216 average time/residue: 0.2520 time to fit residues: 75.8664 Evaluate side-chains 199 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 169 time to evaluate : 2.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 226 CYS Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 0.1980 chunk 102 optimal weight: 5.9990 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN B 295 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9277 Z= 0.275 Angle : 0.622 9.661 12593 Z= 0.321 Chirality : 0.045 0.224 1404 Planarity : 0.004 0.040 1599 Dihedral : 6.280 84.229 1274 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 4.26 % Allowed : 15.55 % Favored : 80.19 % 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: -1.79 (0.24), residues: 1130 helix: 0.19 (0.23), residues: 474 sheet: -1.98 (0.31), residues: 219 loop : -2.25 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 297 HIS 0.006 0.001 HIS B 142 PHE 0.021 0.002 PHE B 199 TYR 0.019 0.002 TYR R 242 ARG 0.007 0.001 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 188 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.7002 (tp) REVERT: R 262 GLU cc_start: 0.7619 (tp30) cc_final: 0.7155 (mp0) REVERT: R 289 TYR cc_start: 0.7919 (t80) cc_final: 0.7523 (t80) REVERT: R 304 ASN cc_start: 0.7335 (m-40) cc_final: 0.5968 (t0) REVERT: R 369 PHE cc_start: 0.4769 (t80) cc_final: 0.3601 (t80) REVERT: R 373 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7819 (mp0) REVERT: A 270 LEU cc_start: 0.9001 (OUTLIER) cc_final: 0.8699 (mp) REVERT: A 338 LYS cc_start: 0.8529 (ttpm) cc_final: 0.8253 (ttpp) REVERT: B 10 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8065 (tm-30) REVERT: B 132 ASN cc_start: 0.6154 (t0) cc_final: 0.5927 (t0) REVERT: B 200 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8692 (p) REVERT: B 211 TRP cc_start: 0.8871 (m100) cc_final: 0.8409 (m100) REVERT: G 46 LYS cc_start: 0.8429 (mppt) cc_final: 0.8121 (mmtm) REVERT: G 48 ASP cc_start: 0.8318 (t70) cc_final: 0.8063 (t0) REVERT: N 105 ARG cc_start: 0.6229 (mtp-110) cc_final: 0.5914 (mtp-110) outliers start: 40 outliers final: 30 residues processed: 210 average time/residue: 0.2588 time to fit residues: 75.5319 Evaluate side-chains 213 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 179 time to evaluate : 1.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 218 LEU Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 309 ILE Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 44 optimal weight: 8.9990 chunk 92 optimal weight: 0.5980 chunk 74 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9277 Z= 0.252 Angle : 0.617 11.345 12593 Z= 0.316 Chirality : 0.044 0.234 1404 Planarity : 0.004 0.040 1599 Dihedral : 6.172 84.606 1273 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 5.01 % Allowed : 17.47 % Favored : 77.53 % 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: -1.49 (0.24), residues: 1130 helix: 0.42 (0.24), residues: 472 sheet: -1.85 (0.32), residues: 213 loop : -2.03 (0.27), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP R 297 HIS 0.005 0.001 HIS B 142 PHE 0.017 0.002 PHE B 199 TYR 0.018 0.002 TYR R 242 ARG 0.008 0.001 ARG N 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 182 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7000 (tp) REVERT: R 202 LYS cc_start: 0.7950 (tptm) cc_final: 0.7731 (tptt) REVERT: R 262 GLU cc_start: 0.7572 (tp30) cc_final: 0.7156 (mp0) REVERT: R 289 TYR cc_start: 0.7877 (t80) cc_final: 0.7524 (t80) REVERT: R 303 MET cc_start: 0.7922 (mmt) cc_final: 0.7413 (mmm) REVERT: R 304 ASN cc_start: 0.7367 (m-40) cc_final: 0.6052 (t0) REVERT: R 369 PHE cc_start: 0.4894 (t80) cc_final: 0.3639 (t80) REVERT: R 373 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: A 270 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8648 (mp) REVERT: A 338 LYS cc_start: 0.8497 (ttpm) cc_final: 0.8172 (ttpp) REVERT: B 10 GLU cc_start: 0.8522 (tm-30) cc_final: 0.8007 (tm-30) REVERT: B 132 ASN cc_start: 0.6118 (t0) cc_final: 0.5895 (t0) REVERT: B 200 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8666 (p) REVERT: B 211 TRP cc_start: 0.8857 (m100) cc_final: 0.8394 (m100) REVERT: G 19 LEU cc_start: 0.8546 (mt) cc_final: 0.8294 (mt) REVERT: G 48 ASP cc_start: 0.8341 (t70) cc_final: 0.8076 (t0) REVERT: N 105 ARG cc_start: 0.6266 (mtp-110) cc_final: 0.5955 (mtp-110) outliers start: 47 outliers final: 31 residues processed: 208 average time/residue: 0.2229 time to fit residues: 63.3321 Evaluate side-chains 208 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 173 time to evaluate : 1.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 213 GLN Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9277 Z= 0.240 Angle : 0.601 8.613 12593 Z= 0.310 Chirality : 0.044 0.241 1404 Planarity : 0.004 0.037 1599 Dihedral : 6.079 85.328 1273 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 5.22 % Allowed : 18.42 % Favored : 76.36 % 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: -1.27 (0.24), residues: 1130 helix: 0.61 (0.24), residues: 471 sheet: -1.73 (0.32), residues: 213 loop : -1.91 (0.28), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 297 HIS 0.006 0.001 HIS A 357 PHE 0.016 0.002 PHE P 28 TYR 0.015 0.002 TYR R 242 ARG 0.004 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 176 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6981 (tp) REVERT: R 262 GLU cc_start: 0.7530 (tp30) cc_final: 0.7129 (mp0) REVERT: R 289 TYR cc_start: 0.7897 (t80) cc_final: 0.7580 (t80) REVERT: R 304 ASN cc_start: 0.7421 (m-40) cc_final: 0.6060 (t0) REVERT: R 369 PHE cc_start: 0.4889 (t80) cc_final: 0.3578 (t80) REVERT: R 373 GLU cc_start: 0.8059 (OUTLIER) cc_final: 0.7624 (mp0) REVERT: A 270 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8658 (mp) REVERT: A 338 LYS cc_start: 0.8496 (ttpm) cc_final: 0.8108 (ttpp) REVERT: B 10 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7995 (tm-30) REVERT: B 85 TYR cc_start: 0.7903 (m-10) cc_final: 0.7619 (m-80) REVERT: B 132 ASN cc_start: 0.6153 (t0) cc_final: 0.5933 (t0) REVERT: B 200 VAL cc_start: 0.8945 (OUTLIER) cc_final: 0.8653 (p) REVERT: B 211 TRP cc_start: 0.8808 (m100) cc_final: 0.8405 (m100) REVERT: G 48 ASP cc_start: 0.8362 (t70) cc_final: 0.8089 (t0) REVERT: N 35 ASN cc_start: 0.7818 (m-40) cc_final: 0.7610 (m110) REVERT: N 105 ARG cc_start: 0.6301 (mtp-110) cc_final: 0.6006 (mtp-110) outliers start: 49 outliers final: 32 residues processed: 206 average time/residue: 0.2174 time to fit residues: 62.0849 Evaluate side-chains 202 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 166 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 353 THR Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 303 ASP Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 79 optimal weight: 0.0970 chunk 91 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9277 Z= 0.172 Angle : 0.580 9.756 12593 Z= 0.296 Chirality : 0.042 0.246 1404 Planarity : 0.003 0.037 1599 Dihedral : 5.749 85.377 1271 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.37 % Allowed : 20.02 % Favored : 75.61 % 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: -1.05 (0.25), residues: 1130 helix: 0.81 (0.24), residues: 472 sheet: -1.60 (0.32), residues: 221 loop : -1.83 (0.28), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.018 0.001 PHE P 28 TYR 0.014 0.001 TYR R 145 ARG 0.005 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 181 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 262 GLU cc_start: 0.7437 (tp30) cc_final: 0.7090 (mp0) REVERT: R 289 TYR cc_start: 0.7863 (t80) cc_final: 0.7533 (t80) REVERT: R 304 ASN cc_start: 0.7373 (m-40) cc_final: 0.6143 (t0) REVERT: R 369 PHE cc_start: 0.4901 (t80) cc_final: 0.3653 (t80) REVERT: R 373 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7600 (mp0) REVERT: A 270 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8605 (mp) REVERT: A 338 LYS cc_start: 0.8447 (ttpm) cc_final: 0.8069 (ttpp) REVERT: B 10 GLU cc_start: 0.8467 (tm-30) cc_final: 0.7985 (tm-30) REVERT: B 61 MET cc_start: 0.8220 (ppp) cc_final: 0.7634 (ptt) REVERT: B 85 TYR cc_start: 0.7854 (m-10) cc_final: 0.7622 (m-80) REVERT: B 132 ASN cc_start: 0.6113 (t0) cc_final: 0.5890 (t0) REVERT: B 200 VAL cc_start: 0.8909 (OUTLIER) cc_final: 0.8669 (p) REVERT: B 211 TRP cc_start: 0.8775 (m100) cc_final: 0.8392 (m100) REVERT: G 48 ASP cc_start: 0.8365 (t70) cc_final: 0.8091 (t0) REVERT: N 70 ILE cc_start: 0.7848 (OUTLIER) cc_final: 0.7602 (pt) REVERT: N 105 ARG cc_start: 0.6336 (mtp-110) cc_final: 0.6049 (mtp-110) outliers start: 41 outliers final: 28 residues processed: 206 average time/residue: 0.2144 time to fit residues: 60.9355 Evaluate side-chains 198 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 166 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 147 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 278 LEU Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 70 ILE Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 93 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 68 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 53 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 GLN B 6 GLN ** B 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9277 Z= 0.258 Angle : 0.622 9.342 12593 Z= 0.320 Chirality : 0.044 0.247 1404 Planarity : 0.004 0.037 1599 Dihedral : 5.789 85.104 1271 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 4.15 % Allowed : 21.73 % Favored : 74.12 % 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 (0.25), residues: 1130 helix: 0.81 (0.24), residues: 474 sheet: -1.47 (0.32), residues: 227 loop : -1.74 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.037 0.002 PHE B 199 TYR 0.014 0.002 TYR R 242 ARG 0.007 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 168 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 LEU cc_start: 0.7289 (OUTLIER) cc_final: 0.7035 (tp) REVERT: R 289 TYR cc_start: 0.7865 (t80) cc_final: 0.7648 (t80) REVERT: R 304 ASN cc_start: 0.7437 (m-40) cc_final: 0.6154 (t0) REVERT: R 369 PHE cc_start: 0.5107 (t80) cc_final: 0.3770 (t80) REVERT: R 373 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: A 270 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8609 (mp) REVERT: A 338 LYS cc_start: 0.8484 (ttpm) cc_final: 0.8094 (ttpp) REVERT: B 10 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8032 (tm-30) REVERT: B 61 MET cc_start: 0.8258 (ppp) cc_final: 0.7650 (ptt) REVERT: B 85 TYR cc_start: 0.8001 (m-10) cc_final: 0.7793 (m-80) REVERT: B 132 ASN cc_start: 0.6150 (t0) cc_final: 0.5937 (t0) REVERT: B 200 VAL cc_start: 0.8857 (OUTLIER) cc_final: 0.8583 (p) REVERT: B 211 TRP cc_start: 0.8835 (m100) cc_final: 0.8468 (m100) REVERT: G 48 ASP cc_start: 0.8376 (t70) cc_final: 0.8117 (t0) outliers start: 39 outliers final: 25 residues processed: 194 average time/residue: 0.2129 time to fit residues: 57.1493 Evaluate side-chains 194 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 165 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.0070 chunk 100 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 0.0870 chunk 106 optimal weight: 3.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9277 Z= 0.235 Angle : 0.629 12.537 12593 Z= 0.319 Chirality : 0.044 0.256 1404 Planarity : 0.004 0.037 1599 Dihedral : 5.702 85.020 1269 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.62 % Allowed : 22.04 % Favored : 74.33 % 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: -0.83 (0.25), residues: 1130 helix: 0.93 (0.24), residues: 468 sheet: -1.50 (0.32), residues: 233 loop : -1.59 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.071 0.002 TRP R 297 HIS 0.005 0.001 HIS A 357 PHE 0.033 0.002 PHE B 199 TYR 0.013 0.002 TYR R 145 ARG 0.007 0.000 ARG B 8 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 166 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 192 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6978 (tp) REVERT: R 289 TYR cc_start: 0.7819 (t80) cc_final: 0.7547 (t80) REVERT: R 304 ASN cc_start: 0.7360 (m-40) cc_final: 0.6081 (t0) REVERT: R 373 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7640 (mp0) REVERT: A 270 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8612 (mp) REVERT: A 338 LYS cc_start: 0.8472 (ttpm) cc_final: 0.8091 (ttpp) REVERT: B 10 GLU cc_start: 0.8544 (tm-30) cc_final: 0.8003 (tm-30) REVERT: B 118 ASP cc_start: 0.8394 (p0) cc_final: 0.8127 (p0) REVERT: B 200 VAL cc_start: 0.8868 (OUTLIER) cc_final: 0.8621 (p) REVERT: B 211 TRP cc_start: 0.8787 (m100) cc_final: 0.8490 (m100) REVERT: G 13 ARG cc_start: 0.7694 (mmt90) cc_final: 0.7443 (ptp-110) REVERT: G 48 ASP cc_start: 0.8372 (t70) cc_final: 0.8098 (t0) outliers start: 34 outliers final: 28 residues processed: 189 average time/residue: 0.2146 time to fit residues: 55.8841 Evaluate side-chains 191 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 159 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 146 ILE Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 271 SER Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 279 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 9 optimal weight: 0.0060 chunk 68 optimal weight: 0.5980 chunk 54 optimal weight: 0.2980 chunk 70 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9277 Z= 0.170 Angle : 0.613 15.923 12593 Z= 0.309 Chirality : 0.043 0.256 1404 Planarity : 0.003 0.041 1599 Dihedral : 5.559 84.028 1269 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer: Outliers : 3.09 % Allowed : 23.43 % Favored : 73.48 % 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: -0.67 (0.25), residues: 1130 helix: 1.07 (0.24), residues: 469 sheet: -1.34 (0.33), residues: 241 loop : -1.57 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP R 297 HIS 0.005 0.001 HIS P 7 PHE 0.030 0.001 PHE B 199 TYR 0.016 0.001 TYR B 289 ARG 0.007 0.000 ARG B 8 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2260 Ramachandran restraints generated. 1130 Oldfield, 0 Emsley, 1130 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 177 time to evaluate : 1.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 213 GLN cc_start: 0.6412 (pm20) cc_final: 0.6181 (pm20) REVERT: R 304 ASN cc_start: 0.7489 (m-40) cc_final: 0.6296 (t0) REVERT: R 373 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: A 270 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8592 (mp) REVERT: A 338 LYS cc_start: 0.8439 (ttpm) cc_final: 0.8062 (ttpp) REVERT: B 10 GLU cc_start: 0.8490 (tm-30) cc_final: 0.7987 (tm-30) REVERT: B 61 MET cc_start: 0.8164 (ppp) cc_final: 0.7722 (ptt) REVERT: B 200 VAL cc_start: 0.8893 (OUTLIER) cc_final: 0.8648 (p) REVERT: G 48 ASP cc_start: 0.8368 (t70) cc_final: 0.8061 (t0) outliers start: 29 outliers final: 23 residues processed: 195 average time/residue: 0.2291 time to fit residues: 60.4745 Evaluate side-chains 186 residues out of total 1001 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 160 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 192 LEU Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain R residue 265 ILE Chi-restraints excluded: chain R residue 307 LEU Chi-restraints excluded: chain R residue 345 ILE Chi-restraints excluded: chain R residue 359 LEU Chi-restraints excluded: chain R residue 373 GLU Chi-restraints excluded: chain R residue 411 LEU Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 218 ASN Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 295 ASP Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 22 CYS Chi-restraints excluded: chain N residue 80 TYR Chi-restraints excluded: chain N residue 91 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.0050 chunk 13 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.165944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.132986 restraints weight = 12063.258| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 2.40 r_work: 0.3562 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9277 Z= 0.189 Angle : 0.629 15.815 12593 Z= 0.316 Chirality : 0.043 0.256 1404 Planarity : 0.004 0.054 1599 Dihedral : 5.531 81.985 1269 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 3.30 % Allowed : 23.54 % Favored : 73.16 % 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: -0.59 (0.25), residues: 1130 helix: 1.18 (0.25), residues: 460 sheet: -1.29 (0.33), residues: 242 loop : -1.52 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 297 HIS 0.004 0.001 HIS A 357 PHE 0.030 0.001 PHE B 199 TYR 0.024 0.002 TYR R 289 ARG 0.007 0.000 ARG B 8 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2444.26 seconds wall clock time: 45 minutes 0.61 seconds (2700.61 seconds total)