Starting phenix.real_space_refine on Wed Feb 14 10:06:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/02_2024/8t3q_41008_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/02_2024/8t3q_41008.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/02_2024/8t3q_41008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/02_2024/8t3q_41008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/02_2024/8t3q_41008_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/02_2024/8t3q_41008_updated.pdb" } resolution = 3.14 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= 0.034 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 55 5.16 5 C 5752 2.51 5 N 1562 2.21 5 O 1666 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 151": "OE1" <-> "OE2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "N GLU 223": "OE1" <-> "OE2" Residue "N GLU 235": "OE1" <-> "OE2" Residue "G GLU 47": "OE1" <-> "OE2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "R ARG 24": "NH1" <-> "NH2" Residue "R PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 99": "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: 9035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1800 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "B" Number of atoms: 2622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2622 Classifications: {'peptide': 342} Link IDs: {'PTRANS': 5, 'TRANS': 336} Chain: "N" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 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: "R" Number of atoms: 2372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2372 Classifications: {'peptide': 298} Link IDs: {'PTRANS': 12, 'TRANS': 285} Chain breaks: 2 Chain: "R" Number of atoms: 24 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 24 Unusual residues: {'HXA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.19, per 1000 atoms: 0.57 Number of scatterers: 9035 At special positions: 0 Unit cell: (85.284, 124.2, 125.856, 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 55 16.00 O 1666 8.00 N 1562 7.00 C 5752 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=2.03 Simple disulfide: pdb=" SG CYS N 160 " - pdb=" SG CYS N 230 " distance=2.03 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 194 " 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: 3.73 Conformation dependent library (CDL) restraints added in 1.9 seconds 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2174 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 13 sheets defined 33.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.81 Creating SS restraints... Processing helix chain 'A' and resid 7 through 31 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 96 through 98 No H-bonds generated for 'chain 'A' and resid 96 through 98' Processing helix chain 'A' and resid 118 through 129 Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 165 through 169 Processing helix chain 'A' and resid 184 through 203 Processing helix chain 'A' and resid 224 through 242 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 4.550A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'G' and resid 7 through 23 removed outlier: 3.751A 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 'R' and resid 36 through 71 removed outlier: 3.568A pdb=" N VAL R 63 " --> pdb=" O VAL R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 78 through 90 removed outlier: 3.587A pdb=" N SER R 90 " --> pdb=" O LEU R 86 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 101 removed outlier: 3.653A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 108 through 139 removed outlier: 3.539A pdb=" N LEU R 113 " --> pdb=" O VAL R 109 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LEU R 114 " --> pdb=" O ALA R 110 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N PHE R 115 " --> pdb=" O CYS R 111 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR R 119 " --> pdb=" O PHE R 115 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER R 123 " --> pdb=" O THR R 119 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N LEU R 127 " --> pdb=" O SER R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 175 Proline residue: R 172 - end of helix Processing helix chain 'R' and resid 201 through 215 Processing helix chain 'R' and resid 217 through 244 removed outlier: 3.534A pdb=" N LEU R 231 " --> pdb=" O TYR R 227 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N THR R 234 " --> pdb=" O ILE R 230 " (cutoff:3.500A) Processing helix chain 'R' and resid 249 through 255 Processing helix chain 'R' and resid 259 through 292 Proline residue: R 279 - end of helix removed outlier: 3.973A pdb=" N PHE R 292 " --> pdb=" O LEU R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 321 removed outlier: 3.824A pdb=" N SER R 314 " --> pdb=" O THR R 310 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA R 315 " --> pdb=" O PHE R 311 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 316 " --> pdb=" O ALA R 312 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 72 through 76 Processing sheet with id= B, first strand: chain 'A' and resid 105 through 111 removed outlier: 6.829A pdb=" N SER A 138 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N PHE A 108 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE A 140 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 110 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N PHE A 142 " --> pdb=" O VAL A 110 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.805A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 102 through 105 removed outlier: 5.924A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.744A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.700A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.626A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.933A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.924A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 294 through 298 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 45 through 51 removed outlier: 3.531A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN B 340 " --> pdb=" O ARG B 46 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= K, first strand: chain 'N' and resid 92 through 97 removed outlier: 5.639A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ALA N 40 " --> pdb=" O LEU N 45 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N LEU N 45 " --> pdb=" O ALA N 40 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'N' and resid 156 through 160 Processing sheet with id= M, first strand: chain 'N' and resid 244 through 246 removed outlier: 6.278A pdb=" N LEU N 179 " --> pdb=" O LEU N 188 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N LEU N 188 " --> pdb=" O LEU N 179 " (cutoff:3.500A) 390 hydrogen bonds defined for protein. 1125 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: 2.52 Time building geometry restraints manager: 3.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1476 1.32 - 1.44: 2522 1.44 - 1.57: 5141 1.57 - 1.69: 0 1.69 - 1.81: 79 Bond restraints: 9218 Sorted by residual: bond pdb=" C HIS R 112 " pdb=" O HIS R 112 " ideal model delta sigma weight residual 1.236 1.313 -0.076 1.15e-02 7.56e+03 4.42e+01 bond pdb=" N VAL R 124 " pdb=" CA VAL R 124 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.08e-02 8.57e+03 1.35e+01 bond pdb=" N VAL R 117 " pdb=" CA VAL R 117 " ideal model delta sigma weight residual 1.460 1.501 -0.041 1.19e-02 7.06e+03 1.20e+01 bond pdb=" N VAL B 112 " pdb=" CA VAL B 112 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.11e-02 8.12e+03 1.19e+01 bond pdb=" C PRO R 108 " pdb=" O PRO R 108 " ideal model delta sigma weight residual 1.237 1.195 0.043 1.26e-02 6.30e+03 1.14e+01 ... (remaining 9213 not shown) Histogram of bond angle deviations from ideal: 98.94 - 106.04: 183 106.04 - 113.15: 4973 113.15 - 120.26: 3786 120.26 - 127.37: 3473 127.37 - 134.47: 87 Bond angle restraints: 12502 Sorted by residual: angle pdb=" N PRO N 237 " pdb=" CA PRO N 237 " pdb=" C PRO N 237 " ideal model delta sigma weight residual 110.95 99.26 11.69 1.62e+00 3.81e-01 5.21e+01 angle pdb=" N LEU R 120 " pdb=" CA LEU R 120 " pdb=" C LEU R 120 " ideal model delta sigma weight residual 113.12 105.33 7.79 1.25e+00 6.40e-01 3.88e+01 angle pdb=" N GLN R 290 " pdb=" CA GLN R 290 " pdb=" C GLN R 290 " ideal model delta sigma weight residual 112.23 104.42 7.81 1.26e+00 6.30e-01 3.84e+01 angle pdb=" N VAL R 124 " pdb=" CA VAL R 124 " pdb=" C VAL R 124 " ideal model delta sigma weight residual 113.42 106.79 6.63 1.17e+00 7.31e-01 3.21e+01 angle pdb=" C PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta sigma weight residual 109.80 100.71 9.09 1.64e+00 3.72e-01 3.07e+01 ... (remaining 12497 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 4884 17.15 - 34.31: 438 34.31 - 51.46: 125 51.46 - 68.62: 23 68.62 - 85.77: 7 Dihedral angle restraints: 5477 sinusoidal: 2119 harmonic: 3358 Sorted by residual: dihedral pdb=" CB CYS R 111 " pdb=" SG CYS R 111 " pdb=" SG CYS R 194 " pdb=" CB CYS R 194 " ideal model delta sinusoidal sigma weight residual 93.00 157.25 -64.25 1 1.00e+01 1.00e-02 5.43e+01 dihedral pdb=" C TYR N 236 " pdb=" N TYR N 236 " pdb=" CA TYR N 236 " pdb=" CB TYR N 236 " ideal model delta harmonic sigma weight residual -122.60 -136.52 13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CA TYR N 236 " pdb=" CB TYR N 236 " ideal model delta harmonic sigma weight residual 122.80 135.12 -12.32 0 2.50e+00 1.60e-01 2.43e+01 ... (remaining 5474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.100: 1197 0.100 - 0.200: 214 0.200 - 0.300: 25 0.300 - 0.401: 1 0.401 - 0.501: 1 Chirality restraints: 1438 Sorted by residual: chirality pdb=" CA TYR N 236 " pdb=" N TYR N 236 " pdb=" C TYR N 236 " pdb=" CB TYR N 236 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.27e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA PHE B 151 " pdb=" N PHE B 151 " pdb=" C PHE B 151 " pdb=" CB PHE B 151 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 1435 not shown) Planarity restraints: 1589 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 HXA R 401 " 0.098 2.00e-02 2.50e+03 2.26e-01 5.11e+02 pdb=" C4 HXA R 401 " -0.301 2.00e-02 2.50e+03 pdb=" C5 HXA R 401 " 0.306 2.00e-02 2.50e+03 pdb=" C6 HXA R 401 " -0.102 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C6 HXA R 401 " -0.069 2.00e-02 2.50e+03 1.33e-01 1.77e+02 pdb=" C7 HXA R 401 " 0.175 2.00e-02 2.50e+03 pdb=" C8 HXA R 401 " -0.175 2.00e-02 2.50e+03 pdb=" C9 HXA R 401 " 0.069 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 HXA R 401 " 0.102 2.00e-02 2.50e+03 1.02e-01 1.04e+02 pdb=" C19 HXA R 401 " -0.101 2.00e-02 2.50e+03 pdb=" C20 HXA R 401 " -0.103 2.00e-02 2.50e+03 pdb=" C21 HXA R 401 " 0.102 2.00e-02 2.50e+03 ... (remaining 1586 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 327 2.69 - 3.25: 8948 3.25 - 3.80: 14389 3.80 - 4.35: 19224 4.35 - 4.90: 31445 Nonbonded interactions: 74333 Sorted by model distance: nonbonded pdb=" OE2 GLU A 8 " pdb=" OH TYR N 176 " model vdw 2.144 2.440 nonbonded pdb=" OG SER B 331 " pdb=" OD1 ASP B 333 " model vdw 2.144 2.440 nonbonded pdb=" OG SER N 157 " pdb=" OG1 THR N 214 " model vdw 2.221 2.440 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.292 2.440 nonbonded pdb=" NE2 HIS B 311 " pdb=" OG1 THR B 329 " model vdw 2.297 2.520 ... (remaining 74328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 3.900 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 27.880 Find NCS groups from input model: 0.260 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6316 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 : 0.008 0.076 9218 Z= 0.526 Angle : 1.151 11.693 12502 Z= 0.813 Chirality : 0.074 0.501 1438 Planarity : 0.009 0.226 1589 Dihedral : 14.658 85.772 3294 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.89 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.29 % Favored : 95.62 % Rotamer: Outliers : 1.75 % Allowed : 16.63 % Favored : 81.62 % Cbeta Deviations : 0.18 % 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 (0.25), residues: 1141 helix: -0.17 (0.27), residues: 375 sheet: -0.39 (0.32), residues: 270 loop : -1.33 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.009 0.002 HIS A 209 PHE 0.021 0.002 PHE B 151 TYR 0.032 0.002 TYR N 236 ARG 0.013 0.001 ARG A 194 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 146 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.6652 (m-40) cc_final: 0.6419 (m-40) REVERT: B 197 ARG cc_start: 0.6821 (mmt180) cc_final: 0.6391 (mmt180) REVERT: B 214 ARG cc_start: 0.7733 (mpt180) cc_final: 0.7266 (ttp80) REVERT: B 217 MET cc_start: 0.6285 (mtt) cc_final: 0.5734 (ptp) REVERT: B 219 ARG cc_start: 0.6923 (mtt-85) cc_final: 0.6638 (mtp85) REVERT: N 235 GLU cc_start: 0.6954 (pt0) cc_final: 0.6604 (mt-10) REVERT: R 22 ARG cc_start: 0.4006 (mmp-170) cc_final: 0.2996 (mpp-170) REVERT: R 24 ARG cc_start: 0.6991 (mtp85) cc_final: 0.6574 (mtp180) REVERT: R 106 LEU cc_start: 0.8623 (mt) cc_final: 0.8415 (mt) REVERT: R 118 MET cc_start: 0.6056 (ttp) cc_final: 0.5672 (mtp) REVERT: R 215 ASN cc_start: 0.8202 (m-40) cc_final: 0.7360 (m-40) outliers start: 17 outliers final: 5 residues processed: 159 average time/residue: 0.2512 time to fit residues: 53.0961 Evaluate side-chains 133 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 HIS A 244 ASN B 9 GLN B 36 ASN B 44 GLN B 88 ASN R 112 HIS R 142 HIS R 182 GLN R 258 GLN ** R 290 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6336 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9218 Z= 0.192 Angle : 0.578 9.470 12502 Z= 0.300 Chirality : 0.042 0.162 1438 Planarity : 0.004 0.076 1589 Dihedral : 6.083 59.775 1280 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.98 % Allowed : 16.43 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.25), residues: 1141 helix: 0.64 (0.27), residues: 376 sheet: -0.50 (0.32), residues: 268 loop : -1.08 (0.27), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 211 HIS 0.004 0.001 HIS N 35 PHE 0.019 0.001 PHE R 27 TYR 0.015 0.001 TYR N 236 ARG 0.008 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 136 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 199 ASP cc_start: 0.6130 (m-30) cc_final: 0.5847 (m-30) REVERT: A 238 MET cc_start: 0.6029 (ttm) cc_final: 0.5736 (ttm) REVERT: A 244 ASN cc_start: 0.7879 (m-40) cc_final: 0.7597 (m-40) REVERT: B 59 TYR cc_start: 0.7147 (m-80) cc_final: 0.5741 (m-80) REVERT: B 197 ARG cc_start: 0.7010 (mmt180) cc_final: 0.6774 (mmt180) REVERT: B 214 ARG cc_start: 0.7750 (mpt180) cc_final: 0.7108 (ttp80) REVERT: B 217 MET cc_start: 0.6228 (mtt) cc_final: 0.5797 (ptp) REVERT: B 277 SER cc_start: 0.8041 (OUTLIER) cc_final: 0.7634 (m) REVERT: R 22 ARG cc_start: 0.3869 (mmp-170) cc_final: 0.2746 (mtm-85) REVERT: R 25 PHE cc_start: 0.7100 (t80) cc_final: 0.6285 (t80) REVERT: R 118 MET cc_start: 0.5736 (ttp) cc_final: 0.5358 (mtp) REVERT: R 137 MET cc_start: 0.6701 (tmm) cc_final: 0.6484 (tmm) REVERT: R 196 LEU cc_start: 0.6758 (mt) cc_final: 0.6050 (mt) REVERT: R 215 ASN cc_start: 0.8031 (m-40) cc_final: 0.7172 (m-40) REVERT: R 290 GLN cc_start: 0.6102 (tp-100) cc_final: 0.5717 (tp40) outliers start: 29 outliers final: 22 residues processed: 157 average time/residue: 0.2078 time to fit residues: 45.2474 Evaluate side-chains 144 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 121 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 117 LEU Chi-restraints excluded: chain N residue 118 THR Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 195 THR Chi-restraints excluded: chain R residue 302 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 57 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 70 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 83 optimal weight: 0.3980 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 44 HIS ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 257 GLN R 290 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9218 Z= 0.315 Angle : 0.628 13.089 12502 Z= 0.322 Chirality : 0.044 0.248 1438 Planarity : 0.004 0.064 1589 Dihedral : 5.866 59.471 1279 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % Rotamer: Outliers : 4.11 % Allowed : 18.17 % Favored : 77.72 % 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: -0.49 (0.25), residues: 1141 helix: 0.88 (0.26), residues: 378 sheet: -0.66 (0.31), residues: 277 loop : -1.01 (0.28), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 211 HIS 0.005 0.001 HIS B 142 PHE 0.018 0.002 PHE R 27 TYR 0.022 0.002 TYR N 236 ARG 0.006 0.001 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 137 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.6077 (ttm) cc_final: 0.5783 (ttm) REVERT: A 244 ASN cc_start: 0.7888 (m-40) cc_final: 0.7558 (m110) REVERT: B 59 TYR cc_start: 0.7483 (m-80) cc_final: 0.6392 (m-80) REVERT: B 197 ARG cc_start: 0.7166 (mmt180) cc_final: 0.6500 (mmt180) REVERT: B 214 ARG cc_start: 0.7744 (mpt180) cc_final: 0.6883 (ttp80) REVERT: B 233 CYS cc_start: 0.7917 (t) cc_final: 0.7693 (t) REVERT: B 277 SER cc_start: 0.7958 (OUTLIER) cc_final: 0.7587 (m) REVERT: B 304 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7575 (ttm110) REVERT: N 236 TYR cc_start: 0.5443 (OUTLIER) cc_final: 0.4792 (t80) REVERT: G 38 MET cc_start: 0.6730 (mmm) cc_final: 0.6524 (mmm) REVERT: R 118 MET cc_start: 0.5663 (OUTLIER) cc_final: 0.5237 (mtp) REVERT: R 137 MET cc_start: 0.6270 (tmm) cc_final: 0.5982 (tmm) REVERT: R 215 ASN cc_start: 0.8142 (m-40) cc_final: 0.7407 (m-40) outliers start: 40 outliers final: 28 residues processed: 166 average time/residue: 0.2104 time to fit residues: 48.4900 Evaluate side-chains 151 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 102 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 29 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6430 moved from start: 0.2523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9218 Z= 0.290 Angle : 0.603 9.753 12502 Z= 0.306 Chirality : 0.043 0.201 1438 Planarity : 0.004 0.058 1589 Dihedral : 5.249 56.983 1276 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 5.24 % Allowed : 17.97 % Favored : 76.80 % 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: -0.43 (0.25), residues: 1141 helix: 1.03 (0.27), residues: 381 sheet: -0.71 (0.31), residues: 287 loop : -1.02 (0.28), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.016 0.002 PHE R 27 TYR 0.017 0.002 TYR N 236 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 138 time to evaluate : 1.016 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7039 (pp30) cc_final: 0.6836 (pp30) REVERT: A 199 ASP cc_start: 0.6102 (m-30) cc_final: 0.5885 (m-30) REVERT: B 59 TYR cc_start: 0.7482 (m-80) cc_final: 0.6425 (m-80) REVERT: B 197 ARG cc_start: 0.7085 (mmt180) cc_final: 0.6663 (mmt180) REVERT: B 214 ARG cc_start: 0.7533 (mpt180) cc_final: 0.6974 (ttp80) REVERT: B 277 SER cc_start: 0.7976 (OUTLIER) cc_final: 0.7768 (m) REVERT: N 82 GLN cc_start: 0.7172 (tp40) cc_final: 0.6971 (tp40) REVERT: N 161 ARG cc_start: 0.7029 (ttp-110) cc_final: 0.6629 (mtm110) REVERT: N 236 TYR cc_start: 0.5378 (OUTLIER) cc_final: 0.4638 (t80) REVERT: R 25 PHE cc_start: 0.7177 (t80) cc_final: 0.6468 (t80) REVERT: R 118 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.5262 (mtp) REVERT: R 137 MET cc_start: 0.6122 (tmm) cc_final: 0.5798 (tmm) REVERT: R 215 ASN cc_start: 0.8108 (m-40) cc_final: 0.7387 (m-40) outliers start: 51 outliers final: 31 residues processed: 176 average time/residue: 0.2166 time to fit residues: 52.2977 Evaluate side-chains 164 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 130 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 163 SER Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 224 VAL Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 91 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 1 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN N 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6400 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9218 Z= 0.175 Angle : 0.562 9.509 12502 Z= 0.282 Chirality : 0.041 0.183 1438 Planarity : 0.004 0.053 1589 Dihedral : 5.001 59.373 1276 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.08 % Allowed : 20.12 % Favored : 76.80 % 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: -0.23 (0.25), residues: 1141 helix: 1.19 (0.27), residues: 382 sheet: -0.45 (0.32), residues: 271 loop : -0.99 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS N 35 PHE 0.013 0.001 PHE R 27 TYR 0.013 0.001 TYR N 236 ARG 0.006 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 129 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 20 ASP cc_start: 0.7158 (m-30) cc_final: 0.6916 (m-30) REVERT: B 59 TYR cc_start: 0.7364 (m-80) cc_final: 0.6387 (m-80) REVERT: B 197 ARG cc_start: 0.7126 (mmt180) cc_final: 0.6667 (mmt180) REVERT: B 214 ARG cc_start: 0.7505 (mpt180) cc_final: 0.6927 (ttp80) REVERT: B 228 ASP cc_start: 0.7399 (OUTLIER) cc_final: 0.6920 (p0) REVERT: B 316 SER cc_start: 0.7908 (t) cc_final: 0.7692 (p) REVERT: N 82 GLN cc_start: 0.7058 (tp40) cc_final: 0.6849 (tp40) REVERT: N 161 ARG cc_start: 0.7091 (ttp-110) cc_final: 0.6654 (mtm110) REVERT: N 236 TYR cc_start: 0.5026 (OUTLIER) cc_final: 0.4344 (t80) REVERT: R 25 PHE cc_start: 0.7103 (t80) cc_final: 0.6209 (t80) REVERT: R 118 MET cc_start: 0.5659 (ttp) cc_final: 0.5259 (mtp) REVERT: R 137 MET cc_start: 0.6107 (tmm) cc_final: 0.5805 (tmm) REVERT: R 215 ASN cc_start: 0.7951 (m-40) cc_final: 0.7251 (m-40) outliers start: 30 outliers final: 24 residues processed: 152 average time/residue: 0.2224 time to fit residues: 46.1375 Evaluate side-chains 148 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 122 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 37 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 57 optimal weight: 8.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6443 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9218 Z= 0.300 Angle : 0.615 11.129 12502 Z= 0.308 Chirality : 0.043 0.217 1438 Planarity : 0.004 0.052 1589 Dihedral : 5.108 59.109 1276 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 4.41 % Allowed : 20.43 % Favored : 75.15 % 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: -0.36 (0.25), residues: 1141 helix: 1.12 (0.26), residues: 382 sheet: -0.79 (0.31), residues: 287 loop : -0.92 (0.28), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 211 HIS 0.004 0.001 HIS N 35 PHE 0.014 0.002 PHE R 27 TYR 0.018 0.002 TYR N 236 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 135 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7562 (m-80) cc_final: 0.6532 (m-80) REVERT: B 197 ARG cc_start: 0.7086 (mmt180) cc_final: 0.6602 (mmt180) REVERT: B 214 ARG cc_start: 0.7504 (mpt180) cc_final: 0.6912 (ttp80) REVERT: B 228 ASP cc_start: 0.7420 (OUTLIER) cc_final: 0.6884 (p0) REVERT: B 304 ARG cc_start: 0.8251 (ttm170) cc_final: 0.7603 (ttm110) REVERT: N 82 GLN cc_start: 0.7123 (tp40) cc_final: 0.6920 (tp40) REVERT: N 161 ARG cc_start: 0.7106 (ttp-110) cc_final: 0.6766 (mtm110) REVERT: N 236 TYR cc_start: 0.5440 (OUTLIER) cc_final: 0.4757 (t80) REVERT: G 58 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7383 (tm-30) REVERT: R 25 PHE cc_start: 0.7040 (t80) cc_final: 0.6128 (t80) REVERT: R 215 ASN cc_start: 0.7979 (m-40) cc_final: 0.7287 (m-40) outliers start: 43 outliers final: 33 residues processed: 162 average time/residue: 0.2354 time to fit residues: 51.7114 Evaluate side-chains 166 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 131 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 74 ASP Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 134 LEU Chi-restraints excluded: chain R residue 138 VAL Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 217 LEU Chi-restraints excluded: chain R residue 255 VAL Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 106 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 80 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 61 optimal weight: 0.0000 chunk 109 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 0.0870 chunk 67 optimal weight: 0.5980 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN R 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 9218 Z= 0.144 Angle : 0.543 11.298 12502 Z= 0.271 Chirality : 0.041 0.317 1438 Planarity : 0.004 0.055 1589 Dihedral : 4.686 59.686 1276 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.29 % Allowed : 21.25 % Favored : 75.46 % 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: -0.07 (0.25), residues: 1141 helix: 1.37 (0.27), residues: 381 sheet: -0.32 (0.32), residues: 268 loop : -0.96 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 82 HIS 0.003 0.001 HIS N 35 PHE 0.011 0.001 PHE R 27 TYR 0.010 0.001 TYR N 191 ARG 0.009 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6487 (mt) cc_final: 0.6236 (mt) REVERT: A 145 LYS cc_start: 0.6860 (mttp) cc_final: 0.6463 (mttp) REVERT: B 59 TYR cc_start: 0.7458 (m-80) cc_final: 0.6496 (m-80) REVERT: B 134 ARG cc_start: 0.6835 (ptt-90) cc_final: 0.6628 (ptt-90) REVERT: B 197 ARG cc_start: 0.7079 (mmt180) cc_final: 0.6628 (mmt180) REVERT: B 214 ARG cc_start: 0.7487 (mpt180) cc_final: 0.6882 (ttp80) REVERT: B 228 ASP cc_start: 0.7454 (OUTLIER) cc_final: 0.6982 (p0) REVERT: B 254 ASP cc_start: 0.7254 (t0) cc_final: 0.6945 (t0) REVERT: N 18 ARG cc_start: 0.7658 (tpt-90) cc_final: 0.7321 (tpt-90) REVERT: N 82 GLN cc_start: 0.7076 (tp40) cc_final: 0.6870 (tp40) REVERT: N 161 ARG cc_start: 0.7120 (ttp-110) cc_final: 0.6734 (mtm110) REVERT: N 236 TYR cc_start: 0.4723 (OUTLIER) cc_final: 0.4125 (t80) REVERT: G 58 GLU cc_start: 0.7636 (tm-30) cc_final: 0.7389 (tm-30) REVERT: R 25 PHE cc_start: 0.7178 (t80) cc_final: 0.6164 (t80) REVERT: R 137 MET cc_start: 0.6076 (tmm) cc_final: 0.5817 (tmm) REVERT: R 215 ASN cc_start: 0.7765 (m-40) cc_final: 0.7102 (m-40) outliers start: 32 outliers final: 26 residues processed: 159 average time/residue: 0.2204 time to fit residues: 47.9186 Evaluate side-chains 155 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 160 CYS Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 0.0470 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 86 optimal weight: 0.0770 chunk 99 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.3047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9218 Z= 0.153 Angle : 0.545 10.716 12502 Z= 0.271 Chirality : 0.041 0.273 1438 Planarity : 0.004 0.054 1589 Dihedral : 4.501 59.976 1274 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.29 % Allowed : 21.77 % Favored : 74.95 % 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: 0.04 (0.25), residues: 1141 helix: 1.48 (0.26), residues: 383 sheet: -0.27 (0.32), residues: 269 loop : -0.94 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 82 HIS 0.004 0.001 HIS N 35 PHE 0.010 0.001 PHE R 27 TYR 0.010 0.001 TYR N 191 ARG 0.010 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 LEU cc_start: 0.6603 (mt) cc_final: 0.6361 (mt) REVERT: A 182 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.7206 (mp0) REVERT: B 59 TYR cc_start: 0.7492 (m-80) cc_final: 0.6543 (m-80) REVERT: B 197 ARG cc_start: 0.7119 (mmt180) cc_final: 0.6705 (mmt180) REVERT: B 214 ARG cc_start: 0.7496 (mpt180) cc_final: 0.6892 (ttp80) REVERT: B 228 ASP cc_start: 0.7422 (OUTLIER) cc_final: 0.6956 (p0) REVERT: B 254 ASP cc_start: 0.7240 (t0) cc_final: 0.6950 (t0) REVERT: N 18 ARG cc_start: 0.7642 (tpt-90) cc_final: 0.7285 (tpt-90) REVERT: N 161 ARG cc_start: 0.7141 (ttp-110) cc_final: 0.6756 (mtm110) REVERT: N 203 ARG cc_start: 0.6168 (ptp90) cc_final: 0.5525 (ptt180) REVERT: N 236 TYR cc_start: 0.4843 (OUTLIER) cc_final: 0.4183 (t80) REVERT: R 25 PHE cc_start: 0.7147 (t80) cc_final: 0.6149 (t80) REVERT: R 215 ASN cc_start: 0.7671 (m-40) cc_final: 0.7001 (m-40) outliers start: 32 outliers final: 26 residues processed: 159 average time/residue: 0.2279 time to fit residues: 49.5072 Evaluate side-chains 156 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 182 GLU Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 3.9990 chunk 102 optimal weight: 0.8980 chunk 105 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 92 optimal weight: 0.0070 chunk 67 optimal weight: 0.8980 chunk 108 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN R 112 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9218 Z= 0.198 Angle : 0.566 10.334 12502 Z= 0.283 Chirality : 0.042 0.249 1438 Planarity : 0.004 0.054 1589 Dihedral : 4.532 57.124 1274 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.59 % Allowed : 21.97 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.25), residues: 1141 helix: 1.52 (0.26), residues: 383 sheet: -0.26 (0.32), residues: 269 loop : -0.90 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.003 0.001 HIS N 35 PHE 0.011 0.001 PHE R 27 TYR 0.012 0.001 TYR N 236 ARG 0.007 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 128 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7551 (m-80) cc_final: 0.6591 (m-80) REVERT: B 197 ARG cc_start: 0.7019 (mmt180) cc_final: 0.6585 (mmt180) REVERT: B 214 ARG cc_start: 0.7506 (mpt180) cc_final: 0.6899 (ttp80) REVERT: B 228 ASP cc_start: 0.7407 (OUTLIER) cc_final: 0.6933 (p0) REVERT: B 254 ASP cc_start: 0.7245 (t0) cc_final: 0.6926 (t0) REVERT: N 161 ARG cc_start: 0.7157 (ttp-110) cc_final: 0.6777 (mtm110) REVERT: N 236 TYR cc_start: 0.4995 (OUTLIER) cc_final: 0.4300 (t80) REVERT: R 25 PHE cc_start: 0.7149 (t80) cc_final: 0.6299 (t80) REVERT: R 215 ASN cc_start: 0.7683 (m-40) cc_final: 0.7056 (m-40) outliers start: 35 outliers final: 28 residues processed: 156 average time/residue: 0.2221 time to fit residues: 47.7615 Evaluate side-chains 155 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 125 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 7.9990 chunk 113 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 90 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6467 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9218 Z= 0.403 Angle : 0.662 10.069 12502 Z= 0.337 Chirality : 0.046 0.250 1438 Planarity : 0.004 0.053 1589 Dihedral : 4.989 52.904 1274 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 3.49 % Allowed : 22.28 % Favored : 74.23 % 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: -0.22 (0.25), residues: 1141 helix: 1.28 (0.26), residues: 382 sheet: -0.77 (0.31), residues: 287 loop : -0.84 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.015 0.002 PHE R 88 TYR 0.022 0.002 TYR N 236 ARG 0.008 0.001 ARG B 134 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2282 Ramachandran restraints generated. 1141 Oldfield, 0 Emsley, 1141 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 135 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7680 (m-80) cc_final: 0.6680 (m-80) REVERT: B 214 ARG cc_start: 0.7515 (mpt180) cc_final: 0.6996 (ttp80) REVERT: B 228 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.6915 (p0) REVERT: B 304 ARG cc_start: 0.8213 (ttm170) cc_final: 0.7598 (ttm110) REVERT: N 161 ARG cc_start: 0.7117 (ttp-110) cc_final: 0.6711 (mtm110) REVERT: N 221 GLU cc_start: 0.6642 (mm-30) cc_final: 0.6168 (mm-30) REVERT: N 236 TYR cc_start: 0.5604 (OUTLIER) cc_final: 0.4883 (t80) REVERT: R 25 PHE cc_start: 0.6994 (t80) cc_final: 0.6071 (t80) REVERT: R 215 ASN cc_start: 0.7946 (m-40) cc_final: 0.7296 (m-40) outliers start: 34 outliers final: 29 residues processed: 161 average time/residue: 0.2317 time to fit residues: 50.2919 Evaluate side-chains 165 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 110 VAL Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 142 THR Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 224 ASP Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 231 MET Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain N residue 239 THR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 94 LEU Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 233 ILE Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 313 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 90 optimal weight: 0.0070 chunk 37 optimal weight: 0.7980 chunk 93 optimal weight: 7.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 79 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.175342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.118905 restraints weight = 10019.576| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.77 r_work: 0.3207 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.3365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9218 Z= 0.170 Angle : 0.562 10.354 12502 Z= 0.282 Chirality : 0.042 0.227 1438 Planarity : 0.004 0.054 1589 Dihedral : 4.535 49.766 1274 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 2.98 % Allowed : 22.90 % Favored : 74.13 % 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: 0.02 (0.25), residues: 1141 helix: 1.33 (0.26), residues: 389 sheet: -0.21 (0.33), residues: 255 loop : -0.88 (0.28), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 82 HIS 0.003 0.001 HIS N 35 PHE 0.011 0.001 PHE R 27 TYR 0.013 0.001 TYR N 236 ARG 0.007 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2263.94 seconds wall clock time: 42 minutes 16.21 seconds (2536.21 seconds total)