Starting phenix.real_space_refine on Mon Mar 11 12:42:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8w8a_37350/03_2024/8w8a_37350_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5250 2.51 5 N 1422 2.21 5 O 1525 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 61": "NH1" <-> "NH2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A GLU 182": "OE1" <-> "OE2" Residue "A GLU 222": "OE1" <-> "OE2" Residue "A GLU 244": "OE1" <-> "OE2" Residue "R ARG 83": "NH1" <-> "NH2" Residue "R TYR 90": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 162": "OE1" <-> "OE2" Residue "R PHE 276": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8260 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1934 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 229} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "R" Number of atoms: 2309 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2309 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 17 Unusual residues: {'T5U': 1} Classifications: {'undetermined': 1, 'water': 1} Link IDs: {None: 1} Time building chain proxies: 4.94, per 1000 atoms: 0.60 Number of scatterers: 8260 At special positions: 0 Unit cell: (79.04, 99.84, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1525 8.00 N 1422 7.00 C 5250 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.27 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.35 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.35 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: 3.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 29 helices and 11 sheets defined 39.4% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 13 through 36 Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 96 through 100 Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 160 through 163 No H-bonds generated for 'chain 'A' and resid 160 through 163' Processing helix chain 'A' and resid 165 through 167 No H-bonds generated for 'chain 'A' and resid 165 through 167' Processing helix chain 'A' and resid 184 through 204 removed outlier: 3.690A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.915A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 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 helix chain 'R' and resid 20 through 50 Processing helix chain 'R' and resid 57 through 75 Processing helix chain 'R' and resid 77 through 85 removed outlier: 3.685A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 93 through 126 Processing helix chain 'R' and resid 128 through 134 removed outlier: 3.706A pdb=" N TYR R 131 " --> pdb=" O PRO R 128 " (cutoff:3.500A) removed outlier: 5.735A pdb=" N LYS R 132 " --> pdb=" O LEU R 129 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LYS R 134 " --> pdb=" O TYR R 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 159 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 169 through 179 Processing helix chain 'R' and resid 188 through 198 removed outlier: 3.562A pdb=" N VAL R 192 " --> pdb=" O LYS R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 200 through 231 Processing helix chain 'R' and resid 248 through 275 Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 283 through 305 removed outlier: 3.624A pdb=" N ASN R 296 " --> pdb=" O PHE R 292 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N SER R 297 " --> pdb=" O GLY R 293 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N THR R 298 " --> pdb=" O TYR R 294 " (cutoff:3.500A) Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 309 through 317 Processing sheet with id= A, first strand: chain 'A' and resid 138 through 144 removed outlier: 4.132A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ASN A 80 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.832A pdb=" N LEU A 43 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N HIS A 82 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N LEU A 45 " --> pdb=" O HIS A 82 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE A 84 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N GLY A 47 " --> pdb=" O PHE A 84 " (cutoff:3.500A) removed outlier: 8.772A pdb=" N VAL A 86 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.819A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.852A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.654A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.136A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.719A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.334A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.500A 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: 6.457A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 306 through 308 Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.616A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 6 Processing sheet with id= J, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.320A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'N' and resid 18 through 20 396 hydrogen bonds defined for protein. 1137 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: 2.43 Time building geometry restraints manager: 3.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1394 1.32 - 1.44: 2329 1.44 - 1.56: 4624 1.56 - 1.69: 2 1.69 - 1.81: 92 Bond restraints: 8441 Sorted by residual: bond pdb=" C13 T5U R 401 " pdb=" O01 T5U R 401 " ideal model delta sigma weight residual 1.536 1.375 0.161 2.00e-02 2.50e+03 6.51e+01 bond pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 1.524 1.447 0.077 1.25e-02 6.40e+03 3.78e+01 bond pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 1.528 1.477 0.051 1.04e-02 9.25e+03 2.40e+01 bond pdb=" C09 T5U R 401 " pdb=" O01 T5U R 401 " ideal model delta sigma weight residual 1.308 1.405 -0.097 2.00e-02 2.50e+03 2.33e+01 bond pdb=" C13 T5U R 401 " pdb=" N03 T5U R 401 " ideal model delta sigma weight residual 1.267 1.354 -0.087 2.00e-02 2.50e+03 1.90e+01 ... (remaining 8436 not shown) Histogram of bond angle deviations from ideal: 99.91 - 107.25: 273 107.25 - 114.59: 4896 114.59 - 121.93: 4598 121.93 - 129.27: 1596 129.27 - 136.61: 69 Bond angle restraints: 11432 Sorted by residual: angle pdb=" N ASP N 109 " pdb=" CA ASP N 109 " pdb=" C ASP N 109 " ideal model delta sigma weight residual 109.71 119.49 -9.78 1.41e+00 5.03e-01 4.81e+01 angle pdb=" N ASN A 66 " pdb=" CA ASN A 66 " pdb=" C ASN A 66 " ideal model delta sigma weight residual 111.30 101.74 9.56 1.43e+00 4.89e-01 4.47e+01 angle pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" C CYS N 96 " ideal model delta sigma weight residual 110.17 100.08 10.09 1.61e+00 3.86e-01 3.93e+01 angle pdb=" N GLY A 68 " pdb=" CA GLY A 68 " pdb=" C GLY A 68 " ideal model delta sigma weight residual 112.49 119.46 -6.97 1.21e+00 6.83e-01 3.32e+01 angle pdb=" N HIS A 64 " pdb=" CA HIS A 64 " pdb=" C HIS A 64 " ideal model delta sigma weight residual 110.06 102.44 7.62 1.43e+00 4.89e-01 2.84e+01 ... (remaining 11427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.53: 4576 17.53 - 35.07: 358 35.07 - 52.60: 66 52.60 - 70.14: 14 70.14 - 87.67: 3 Dihedral angle restraints: 5017 sinusoidal: 1970 harmonic: 3047 Sorted by residual: dihedral pdb=" CB CYS R 96 " pdb=" SG CYS R 96 " pdb=" SG CYS R 182 " pdb=" CB CYS R 182 " ideal model delta sinusoidal sigma weight residual 93.00 179.74 -86.74 1 1.00e+01 1.00e-02 9.05e+01 dihedral pdb=" CB CYS N 22 " pdb=" SG CYS N 22 " pdb=" SG CYS N 96 " pdb=" CB CYS N 96 " ideal model delta sinusoidal sigma weight residual 93.00 160.94 -67.94 1 1.00e+01 1.00e-02 5.99e+01 dihedral pdb=" C CYS N 96 " pdb=" N CYS N 96 " pdb=" CA CYS N 96 " pdb=" CB CYS N 96 " ideal model delta harmonic sigma weight residual -122.60 -109.09 -13.51 0 2.50e+00 1.60e-01 2.92e+01 ... (remaining 5014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1024 0.059 - 0.117: 200 0.117 - 0.176: 36 0.176 - 0.234: 9 0.234 - 0.293: 6 Chirality restraints: 1275 Sorted by residual: chirality pdb=" CA LYS A 126 " pdb=" N LYS A 126 " pdb=" C LYS A 126 " pdb=" CB LYS A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CA MET A 60 " pdb=" N MET A 60 " pdb=" C MET A 60 " pdb=" CB MET A 60 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA GLU R 162 " pdb=" N GLU R 162 " pdb=" C GLU R 162 " pdb=" CB GLU R 162 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.96e+00 ... (remaining 1272 not shown) Planarity restraints: 1456 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR N 94 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.91e+00 pdb=" C TYR N 94 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR N 94 " 0.018 2.00e-02 2.50e+03 pdb=" N TYR N 95 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 57 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.19e+00 pdb=" C LYS B 57 " 0.039 2.00e-02 2.50e+03 pdb=" O LYS B 57 " -0.015 2.00e-02 2.50e+03 pdb=" N ILE B 58 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 125 " -0.010 2.00e-02 2.50e+03 2.02e-02 4.09e+00 pdb=" C PHE A 125 " 0.035 2.00e-02 2.50e+03 pdb=" O PHE A 125 " -0.013 2.00e-02 2.50e+03 pdb=" N LYS A 126 " -0.012 2.00e-02 2.50e+03 ... (remaining 1453 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2229 2.80 - 3.33: 7785 3.33 - 3.85: 14077 3.85 - 4.38: 16729 4.38 - 4.90: 29103 Nonbonded interactions: 69923 Sorted by model distance: nonbonded pdb=" NH2 ARG A 90 " pdb=" OD1 ASP B 186 " model vdw 2.280 2.520 nonbonded pdb=" OH TYR B 59 " pdb=" OE1 GLN B 75 " model vdw 2.290 2.440 nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.292 2.440 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.303 2.440 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.320 2.440 ... (remaining 69918 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.930 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.910 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 0.161 8441 Z= 0.400 Angle : 0.725 11.611 11432 Z= 0.430 Chirality : 0.053 0.293 1275 Planarity : 0.004 0.039 1456 Dihedral : 12.966 87.674 3040 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.89 % Allowed : 1.12 % Favored : 97.99 % Cbeta Deviations : 0.10 % 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: 0.81 (0.27), residues: 1033 helix: 2.09 (0.26), residues: 409 sheet: -0.20 (0.35), residues: 213 loop : -0.61 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP R 89 HIS 0.005 0.001 HIS A 209 PHE 0.027 0.002 PHE R 185 TYR 0.016 0.001 TYR N 60 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 167 time to evaluate : 0.947 Fit side-chains REVERT: N 3 GLN cc_start: 0.8194 (pt0) cc_final: 0.7623 (pt0) REVERT: R 60 TRP cc_start: 0.8292 (m100) cc_final: 0.8079 (m100) outliers start: 8 outliers final: 2 residues processed: 174 average time/residue: 1.1533 time to fit residues: 213.5910 Evaluate side-chains 132 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 130 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 225 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 79 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 0.0570 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 59 GLN A 130 ASN A 146 GLN G 24 ASN R 300 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8441 Z= 0.339 Angle : 0.576 6.655 11432 Z= 0.302 Chirality : 0.045 0.164 1275 Planarity : 0.004 0.037 1456 Dihedral : 4.994 48.492 1151 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.24 % Allowed : 11.19 % Favored : 85.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1033 helix: 2.13 (0.26), residues: 409 sheet: -0.29 (0.36), residues: 193 loop : -0.64 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.007 0.001 HIS A 209 PHE 0.015 0.002 PHE B 292 TYR 0.014 0.002 TYR R 90 ARG 0.005 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 131 time to evaluate : 1.032 Fit side-chains REVERT: B 19 ARG cc_start: 0.8038 (ttm110) cc_final: 0.7678 (ttp-110) REVERT: N 3 GLN cc_start: 0.8177 (pt0) cc_final: 0.7568 (pt0) REVERT: R 188 LYS cc_start: 0.8500 (mmtp) cc_final: 0.8276 (mmtp) REVERT: R 302 MET cc_start: 0.7979 (mtt) cc_final: 0.7738 (mtt) outliers start: 29 outliers final: 15 residues processed: 144 average time/residue: 1.1654 time to fit residues: 178.8977 Evaluate side-chains 139 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 124 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 225 SER Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8441 Z= 0.230 Angle : 0.516 9.627 11432 Z= 0.268 Chirality : 0.043 0.165 1275 Planarity : 0.003 0.038 1456 Dihedral : 4.551 48.308 1150 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.46 % Allowed : 14.09 % Favored : 83.45 % 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: 0.85 (0.26), residues: 1033 helix: 2.21 (0.26), residues: 411 sheet: -0.37 (0.35), residues: 196 loop : -0.59 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.012 0.001 PHE B 292 TYR 0.013 0.001 TYR R 308 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 129 time to evaluate : 1.037 Fit side-chains REVERT: N 3 GLN cc_start: 0.8204 (pt0) cc_final: 0.7621 (pt0) REVERT: R 83 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.6273 (ttm170) outliers start: 22 outliers final: 14 residues processed: 139 average time/residue: 1.2012 time to fit residues: 177.8658 Evaluate side-chains 133 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 118 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 97 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8441 Z= 0.188 Angle : 0.487 8.089 11432 Z= 0.253 Chirality : 0.042 0.156 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.357 49.251 1149 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.36 % Allowed : 15.21 % Favored : 81.43 % 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: 1.03 (0.27), residues: 1033 helix: 2.39 (0.26), residues: 404 sheet: -0.19 (0.36), residues: 197 loop : -0.51 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.012 0.001 PHE R 165 TYR 0.013 0.001 TYR R 308 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 130 time to evaluate : 0.938 Fit side-chains REVERT: B 19 ARG cc_start: 0.8045 (ttm110) cc_final: 0.7720 (ttp-110) REVERT: N 3 GLN cc_start: 0.8193 (pt0) cc_final: 0.7611 (pt0) REVERT: R 83 ARG cc_start: 0.7839 (OUTLIER) cc_final: 0.6241 (ttm170) outliers start: 30 outliers final: 16 residues processed: 142 average time/residue: 1.1210 time to fit residues: 170.0816 Evaluate side-chains 137 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 120 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 67 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8441 Z= 0.252 Angle : 0.519 8.152 11432 Z= 0.270 Chirality : 0.043 0.189 1275 Planarity : 0.003 0.038 1456 Dihedral : 4.429 49.205 1149 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.91 % Allowed : 16.33 % Favored : 79.75 % 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: 0.98 (0.26), residues: 1033 helix: 2.34 (0.26), residues: 404 sheet: -0.30 (0.34), residues: 215 loop : -0.50 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.005 0.001 HIS A 209 PHE 0.014 0.001 PHE R 91 TYR 0.016 0.001 TYR N 80 ARG 0.003 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 123 time to evaluate : 0.987 Fit side-chains REVERT: A 132 ARG cc_start: 0.8178 (OUTLIER) cc_final: 0.7839 (ttm110) REVERT: B 19 ARG cc_start: 0.8007 (ttm110) cc_final: 0.7693 (ttp-110) REVERT: N 3 GLN cc_start: 0.8213 (pt0) cc_final: 0.7632 (pt0) REVERT: R 83 ARG cc_start: 0.7851 (OUTLIER) cc_final: 0.6218 (ttm170) REVERT: R 88 CYS cc_start: 0.8083 (t) cc_final: 0.7604 (t) outliers start: 35 outliers final: 18 residues processed: 138 average time/residue: 1.2254 time to fit residues: 179.8972 Evaluate side-chains 135 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 318 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8441 Z= 0.229 Angle : 0.514 11.304 11432 Z= 0.264 Chirality : 0.043 0.161 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.393 48.594 1149 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.58 % Allowed : 16.78 % Favored : 79.64 % 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: 1.01 (0.26), residues: 1033 helix: 2.40 (0.26), residues: 404 sheet: -0.21 (0.35), residues: 205 loop : -0.55 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.011 0.001 PHE B 151 TYR 0.013 0.001 TYR R 308 ARG 0.005 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 1.034 Fit side-chains REVERT: A 132 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7862 (ttm110) REVERT: B 19 ARG cc_start: 0.7991 (ttm110) cc_final: 0.7729 (ttp-110) REVERT: N 3 GLN cc_start: 0.8176 (pt0) cc_final: 0.7587 (pt0) REVERT: R 83 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.6209 (ttm170) outliers start: 32 outliers final: 18 residues processed: 136 average time/residue: 1.2602 time to fit residues: 182.1359 Evaluate side-chains 137 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 117 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 318 MET 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: 7.9990 chunk 71 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 54 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 38 optimal weight: 0.3980 chunk 58 optimal weight: 7.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8441 Z= 0.177 Angle : 0.497 10.119 11432 Z= 0.254 Chirality : 0.042 0.154 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.307 47.849 1149 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.91 % Allowed : 17.90 % Favored : 79.19 % 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: 1.11 (0.27), residues: 1033 helix: 2.51 (0.26), residues: 404 sheet: -0.28 (0.34), residues: 212 loop : -0.46 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.004 0.001 HIS R 63 PHE 0.010 0.001 PHE B 151 TYR 0.016 0.001 TYR N 80 ARG 0.003 0.000 ARG N 118 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.870 Fit side-chains REVERT: A 34 GLU cc_start: 0.7027 (OUTLIER) cc_final: 0.6802 (tt0) REVERT: A 132 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7859 (ttm110) REVERT: N 3 GLN cc_start: 0.8193 (pt0) cc_final: 0.7611 (pt0) REVERT: R 83 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.6156 (ttm170) outliers start: 26 outliers final: 13 residues processed: 135 average time/residue: 1.2403 time to fit residues: 178.0205 Evaluate side-chains 131 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 76 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 93 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8441 Z= 0.168 Angle : 0.504 14.271 11432 Z= 0.253 Chirality : 0.042 0.156 1275 Planarity : 0.003 0.040 1456 Dihedral : 4.256 47.196 1149 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.24 % Allowed : 17.79 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 1033 helix: 2.59 (0.26), residues: 404 sheet: -0.22 (0.34), residues: 217 loop : -0.43 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.013 0.001 PHE R 91 TYR 0.012 0.001 TYR R 308 ARG 0.007 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 121 time to evaluate : 0.965 Fit side-chains REVERT: A 34 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6829 (tt0) REVERT: A 132 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7857 (ttm110) REVERT: B 19 ARG cc_start: 0.8037 (ttm110) cc_final: 0.7624 (ttp-110) REVERT: N 3 GLN cc_start: 0.8185 (pt0) cc_final: 0.7600 (pt0) REVERT: R 83 ARG cc_start: 0.7760 (OUTLIER) cc_final: 0.6145 (ttm170) outliers start: 29 outliers final: 19 residues processed: 136 average time/residue: 1.2296 time to fit residues: 178.8764 Evaluate side-chains 140 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 118 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 34 GLU Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain N residue 37 VAL Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 290 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 59 optimal weight: 2.9990 chunk 95 optimal weight: 0.3980 chunk 58 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8441 Z= 0.211 Angle : 0.526 13.612 11432 Z= 0.264 Chirality : 0.042 0.156 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.304 47.564 1149 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.02 % Allowed : 18.34 % Favored : 78.64 % 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: 1.21 (0.27), residues: 1033 helix: 2.54 (0.26), residues: 404 sheet: -0.27 (0.34), residues: 225 loop : -0.31 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.010 0.001 PHE B 151 TYR 0.013 0.001 TYR N 80 ARG 0.006 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 120 time to evaluate : 0.981 Fit side-chains REVERT: A 132 ARG cc_start: 0.8191 (OUTLIER) cc_final: 0.7864 (ttm110) REVERT: B 19 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7690 (ttp-110) REVERT: N 3 GLN cc_start: 0.8159 (pt0) cc_final: 0.7563 (pt0) REVERT: R 83 ARG cc_start: 0.7768 (OUTLIER) cc_final: 0.6178 (ttm170) outliers start: 27 outliers final: 19 residues processed: 133 average time/residue: 1.2479 time to fit residues: 176.2039 Evaluate side-chains 139 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 100 optimal weight: 1.9990 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 61 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8441 Z= 0.217 Angle : 0.520 13.115 11432 Z= 0.263 Chirality : 0.043 0.157 1275 Planarity : 0.003 0.039 1456 Dihedral : 4.316 47.654 1149 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.68 % Allowed : 18.90 % Favored : 78.41 % 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: 1.14 (0.27), residues: 1033 helix: 2.53 (0.26), residues: 404 sheet: -0.31 (0.34), residues: 222 loop : -0.40 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 169 HIS 0.004 0.001 HIS A 209 PHE 0.016 0.001 PHE R 91 TYR 0.012 0.001 TYR R 308 ARG 0.006 0.000 ARG B 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.006 Fit side-chains REVERT: A 132 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7865 (ttm110) REVERT: N 3 GLN cc_start: 0.8186 (pt0) cc_final: 0.7638 (pt0) REVERT: R 83 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.6191 (ttm170) outliers start: 24 outliers final: 20 residues processed: 129 average time/residue: 1.2023 time to fit residues: 165.1378 Evaluate side-chains 138 residues out of total 900 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 116 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 49 ASP Chi-restraints excluded: chain A residue 65 VAL Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 132 ARG Chi-restraints excluded: chain B residue 36 ASN Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 97 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 268 ASN Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 21 SER Chi-restraints excluded: chain R residue 35 LEU Chi-restraints excluded: chain R residue 83 ARG Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 290 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 80 optimal weight: 6.9990 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 70 optimal weight: 6.9990 chunk 4 optimal weight: 0.2980 chunk 57 optimal weight: 0.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.149168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.111956 restraints weight = 9689.232| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.27 r_work: 0.3204 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8441 Z= 0.165 Angle : 0.500 13.187 11432 Z= 0.251 Chirality : 0.042 0.157 1275 Planarity : 0.003 0.040 1456 Dihedral : 4.227 46.776 1149 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.35 % Allowed : 19.46 % Favored : 78.19 % 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: 1.22 (0.27), residues: 1033 helix: 2.60 (0.26), residues: 404 sheet: -0.25 (0.34), residues: 227 loop : -0.37 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 169 HIS 0.003 0.001 HIS A 209 PHE 0.010 0.001 PHE B 151 TYR 0.012 0.001 TYR R 308 ARG 0.004 0.000 ARG B 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3484.53 seconds wall clock time: 62 minutes 41.64 seconds (3761.64 seconds total)