Starting phenix.real_space_refine on Fri Jul 19 22:20:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/07_2024/8t3q_41008.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/07_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_41008/07_2024/8t3q_41008.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/07_2024/8t3q_41008.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/07_2024/8t3q_41008.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t3q_41008/07_2024/8t3q_41008.cif" } 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-5388/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: 5.53, per 1000 atoms: 0.61 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: 3.44 Conformation dependent library (CDL) restraints added in 1.5 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... Secondary structure from input PDB file: 26 helices and 15 sheets defined 36.6% alpha, 20.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.232A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.724A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 99 removed outlier: 3.759A pdb=" N GLN A 98 " --> pdb=" O LYS A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.953A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 170 Processing helix chain 'A' and resid 183 through 204 removed outlier: 4.106A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 243 Processing helix chain 'B' and resid 3 through 25 removed outlier: 3.949A pdb=" N LEU B 7 " --> pdb=" O GLU B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 53 through 56 removed outlier: 3.532A pdb=" N GLY N 56 " --> pdb=" O SER N 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 53 through 56' Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.751A pdb=" N GLN G 11 " --> pdb=" O ALA G 7 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 35 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 77 through 89 Processing helix chain 'R' and resid 91 through 102 removed outlier: 3.653A pdb=" N THR R 101 " --> pdb=" O ALA R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 140 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 151 through 170 Processing helix chain 'R' and resid 171 through 176 Processing helix chain 'R' and resid 200 through 216 Processing helix chain 'R' and resid 216 through 245 removed outlier: 3.675A pdb=" N GLY R 220 " --> pdb=" O PHE R 216 " (cutoff:3.500A) 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) removed outlier: 3.652A pdb=" N LEU R 245 " --> pdb=" O LEU R 241 " (cutoff:3.500A) Processing helix chain 'R' and resid 248 through 256 Processing helix chain 'R' and resid 258 through 291 Proline residue: R 279 - end of helix Processing helix chain 'R' and resid 299 through 322 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=AA1, first strand: chain 'A' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 39 removed outlier: 3.773A pdb=" N VAL A 109 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 45 through 51 removed outlier: 6.312A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU B 336 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.860A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, 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=AA6, first strand: chain 'B' and resid 146 through 151 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=AA7, first strand: chain 'B' and resid 187 through 192 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=AA8, first strand: chain 'B' and resid 229 through 234 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=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.687A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'N' and resid 11 through 12 Processing sheet with id=AB3, first strand: chain 'N' and resid 58 through 60 removed outlier: 4.952A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 141 through 142 Processing sheet with id=AB5, first strand: chain 'N' and resid 148 through 149 removed outlier: 3.788A pdb=" N VAL N 148 " --> pdb=" O LYS N 245 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N GLU N 247 " --> pdb=" O VAL N 148 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N LEU N 175 " --> pdb=" O TYR N 191 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N TYR N 191 " --> pdb=" O LEU N 175 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP N 177 " --> pdb=" O LEU N 189 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'R' and resid 180 through 181 445 hydrogen bonds defined for protein. 1254 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: 2.42 Time building geometry restraints manager: 3.78 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: 323 2.69 - 3.25: 8908 3.25 - 3.80: 14332 3.80 - 4.35: 19120 4.35 - 4.90: 31430 Nonbonded interactions: 74113 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 74108 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: 0.820 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: 0.390 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.730 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.750 ------------------------------------------------------------------------------- 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= 0.532 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 : 0.978 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: 0.2493 time to fit residues: 52.5923 Evaluate side-chains 133 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.941 ------------------------------------------------------------------------------- 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: 8.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 54 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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: 0.6335 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9218 Z= 0.198 Angle : 0.585 9.525 12502 Z= 0.307 Chirality : 0.042 0.169 1438 Planarity : 0.004 0.076 1589 Dihedral : 6.129 58.897 1280 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 2.87 % Allowed : 16.74 % Favored : 80.39 % 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: -0.55 (0.25), residues: 1141 helix: 0.58 (0.26), residues: 378 sheet: -0.17 (0.33), residues: 254 loop : -1.15 (0.27), residues: 509 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 0.018 0.001 PHE R 27 TYR 0.016 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 162 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 134 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 238 MET cc_start: 0.6037 (ttm) cc_final: 0.5734 (ttm) REVERT: A 244 ASN cc_start: 0.7752 (m-40) cc_final: 0.7476 (m-40) REVERT: B 59 TYR cc_start: 0.7059 (m-80) cc_final: 0.5984 (m-80) REVERT: B 197 ARG cc_start: 0.7020 (mmt180) cc_final: 0.6789 (mmt180) REVERT: B 214 ARG cc_start: 0.7742 (mpt180) cc_final: 0.7099 (ttp80) REVERT: B 217 MET cc_start: 0.6216 (mtt) cc_final: 0.5771 (ptp) REVERT: B 277 SER cc_start: 0.8044 (OUTLIER) cc_final: 0.7632 (m) REVERT: R 22 ARG cc_start: 0.3874 (mmp-170) cc_final: 0.2747 (mtm-85) REVERT: R 25 PHE cc_start: 0.7089 (t80) cc_final: 0.6231 (t80) REVERT: R 118 MET cc_start: 0.5738 (ttp) cc_final: 0.5330 (mtp) REVERT: R 137 MET cc_start: 0.6647 (tmm) cc_final: 0.6408 (tmm) REVERT: R 215 ASN cc_start: 0.7954 (m-40) cc_final: 0.7169 (m-40) REVERT: R 290 GLN cc_start: 0.6091 (tp-100) cc_final: 0.5594 (tp-100) outliers start: 28 outliers final: 22 residues processed: 154 average time/residue: 0.2090 time to fit residues: 44.9360 Evaluate side-chains 145 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 122 time to evaluate : 1.044 ------------------------------------------------------------------------------- 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: 4.9990 chunk 32 optimal weight: 3.9990 chunk 86 optimal weight: 10.0000 chunk 70 optimal weight: 0.0970 chunk 28 optimal weight: 3.9990 chunk 103 optimal weight: 0.0870 chunk 112 optimal weight: 1.9990 chunk 92 optimal weight: 10.0000 chunk 102 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 83 optimal weight: 0.8980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 257 GLN R 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6330 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9218 Z= 0.161 Angle : 0.551 12.966 12502 Z= 0.281 Chirality : 0.041 0.174 1438 Planarity : 0.004 0.064 1589 Dihedral : 5.540 58.106 1279 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.18 % Allowed : 17.56 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.25), residues: 1141 helix: 1.03 (0.26), residues: 384 sheet: -0.12 (0.33), residues: 268 loop : -1.08 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.012 0.001 PHE R 27 TYR 0.013 0.001 TYR N 236 ARG 0.005 0.000 ARG B 96 *********************** 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 168 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 137 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7085 (pp30) cc_final: 0.6812 (pp30) REVERT: A 126 LYS cc_start: 0.6526 (tttp) cc_final: 0.6045 (ttmm) REVERT: A 244 ASN cc_start: 0.7735 (m-40) cc_final: 0.7430 (m110) REVERT: B 191 SER cc_start: 0.7936 (t) cc_final: 0.7479 (t) REVERT: B 197 ARG cc_start: 0.7138 (mmt180) cc_final: 0.6886 (mmt180) REVERT: B 214 ARG cc_start: 0.7732 (mpt180) cc_final: 0.7050 (ttp80) REVERT: B 217 MET cc_start: 0.6472 (mtt) cc_final: 0.6162 (ptp) REVERT: N 236 TYR cc_start: 0.4928 (OUTLIER) cc_final: 0.4143 (t80) REVERT: G 37 LEU cc_start: 0.4401 (OUTLIER) cc_final: 0.4080 (tt) REVERT: R 22 ARG cc_start: 0.4125 (mmp-170) cc_final: 0.2875 (mtm-85) REVERT: R 24 ARG cc_start: 0.6354 (mtp180) cc_final: 0.5830 (mtp180) REVERT: R 25 PHE cc_start: 0.7151 (t80) cc_final: 0.6276 (t80) REVERT: R 118 MET cc_start: 0.5675 (OUTLIER) cc_final: 0.5309 (mtp) REVERT: R 137 MET cc_start: 0.6347 (tmm) cc_final: 0.6142 (tmm) REVERT: R 215 ASN cc_start: 0.7758 (m-40) cc_final: 0.7043 (m-40) outliers start: 31 outliers final: 19 residues processed: 161 average time/residue: 0.2115 time to fit residues: 46.9796 Evaluate side-chains 148 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 GLU Chi-restraints excluded: chain A residue 122 LEU 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 336 LEU Chi-restraints excluded: chain N residue 30 SER 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 163 SER 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 G residue 17 GLU Chi-restraints excluded: chain G residue 37 LEU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 118 MET Chi-restraints excluded: chain R residue 138 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: 5.9990 chunk 77 optimal weight: 5.9990 chunk 53 optimal weight: 0.0010 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.0870 chunk 69 optimal weight: 9.9990 chunk 104 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 chunk 98 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 overall best weight: 1.5568 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2380 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= 0.281 Angle : 0.607 10.383 12502 Z= 0.311 Chirality : 0.043 0.205 1438 Planarity : 0.004 0.057 1589 Dihedral : 5.380 51.999 1278 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 4.93 % Allowed : 17.66 % Favored : 77.41 % 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: -0.24 (0.25), residues: 1141 helix: 1.11 (0.26), residues: 387 sheet: -0.35 (0.32), residues: 274 loop : -1.03 (0.28), residues: 480 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 0.022 0.002 PHE R 303 TYR 0.017 0.002 TYR N 236 ARG 0.006 0.000 ARG N 161 *********************** 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 180 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 132 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7351 (m-80) cc_final: 0.6411 (m-80) REVERT: B 197 ARG cc_start: 0.7187 (mmt180) cc_final: 0.6858 (mmt180) REVERT: B 214 ARG cc_start: 0.7747 (mpt180) cc_final: 0.7106 (ttp80) REVERT: B 304 ARG cc_start: 0.8239 (ttm170) cc_final: 0.7582 (ttm110) REVERT: N 161 ARG cc_start: 0.7165 (ttp-110) cc_final: 0.6778 (mtm110) REVERT: N 236 TYR cc_start: 0.5407 (OUTLIER) cc_final: 0.4681 (t80) REVERT: G 37 LEU cc_start: 0.5096 (OUTLIER) cc_final: 0.4773 (tt) REVERT: R 25 PHE cc_start: 0.7166 (t80) cc_final: 0.6241 (t80) REVERT: R 118 MET cc_start: 0.5651 (OUTLIER) cc_final: 0.5260 (mtp) REVERT: R 137 MET cc_start: 0.6094 (tmm) cc_final: 0.5786 (tmm) REVERT: R 215 ASN cc_start: 0.7919 (m-40) cc_final: 0.7277 (m-40) REVERT: R 294 GLN cc_start: 0.6666 (OUTLIER) cc_final: 0.5902 (pp30) outliers start: 48 outliers final: 32 residues processed: 171 average time/residue: 0.2107 time to fit residues: 49.7824 Evaluate side-chains 159 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 123 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 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 146 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 234 PHE 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 30 SER 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 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 G residue 37 LEU 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 294 GLN 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: 5.9990 chunk 62 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 32 GLN N 143 GLN R 80 ASN ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9218 Z= 0.249 Angle : 0.598 11.752 12502 Z= 0.298 Chirality : 0.042 0.204 1438 Planarity : 0.004 0.053 1589 Dihedral : 5.053 56.837 1276 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.11 % Allowed : 18.79 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.25), residues: 1141 helix: 1.28 (0.26), residues: 388 sheet: -0.60 (0.31), residues: 294 loop : -0.89 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.004 0.001 HIS R 112 PHE 0.018 0.001 PHE R 303 TYR 0.017 0.001 TYR N 236 ARG 0.007 0.000 ARG B 134 *********************** 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 167 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 127 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 166 GLU cc_start: 0.6958 (tp30) cc_final: 0.6751 (tp30) REVERT: B 197 ARG cc_start: 0.7237 (mmt180) cc_final: 0.6889 (mmt180) REVERT: B 214 ARG cc_start: 0.7746 (mpt180) cc_final: 0.7117 (ttp80) REVERT: N 161 ARG cc_start: 0.7216 (ttp-110) cc_final: 0.6822 (mtm110) REVERT: N 236 TYR cc_start: 0.5210 (OUTLIER) cc_final: 0.4490 (t80) REVERT: G 58 GLU cc_start: 0.7884 (tm-30) cc_final: 0.7514 (tm-30) REVERT: R 25 PHE cc_start: 0.7223 (t80) cc_final: 0.6567 (t80) REVERT: R 118 MET cc_start: 0.5656 (OUTLIER) cc_final: 0.5271 (mtp) REVERT: R 137 MET cc_start: 0.5988 (tmm) cc_final: 0.5675 (tmm) REVERT: R 215 ASN cc_start: 0.7883 (m-40) cc_final: 0.7196 (m-40) outliers start: 40 outliers final: 31 residues processed: 159 average time/residue: 0.2238 time to fit residues: 48.5497 Evaluate side-chains 158 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 125 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 136 THR 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 234 PHE 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 30 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 117 LEU 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 194 SER 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 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 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: 5.9990 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 57 optimal weight: 6.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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: 0.6391 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9218 Z= 0.178 Angle : 0.553 10.505 12502 Z= 0.277 Chirality : 0.041 0.171 1438 Planarity : 0.004 0.053 1589 Dihedral : 4.811 59.017 1276 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.00 % Allowed : 18.79 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1141 helix: 1.50 (0.27), residues: 387 sheet: -0.33 (0.32), residues: 278 loop : -0.99 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 211 HIS 0.003 0.001 HIS N 35 PHE 0.016 0.001 PHE R 303 TYR 0.011 0.001 TYR N 236 ARG 0.007 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 170 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLN cc_start: 0.7230 (pp30) cc_final: 0.7002 (pp30) REVERT: B 59 TYR cc_start: 0.7351 (m-80) cc_final: 0.6707 (m-80) REVERT: B 191 SER cc_start: 0.8072 (t) cc_final: 0.7621 (t) REVERT: B 197 ARG cc_start: 0.7320 (mmt180) cc_final: 0.6625 (mmt180) REVERT: B 214 ARG cc_start: 0.7745 (mpt180) cc_final: 0.6869 (ttp80) REVERT: B 233 CYS cc_start: 0.7799 (t) cc_final: 0.7548 (t) REVERT: N 161 ARG cc_start: 0.7203 (ttp-110) cc_final: 0.6812 (mtm110) REVERT: N 236 TYR cc_start: 0.4924 (OUTLIER) cc_final: 0.4168 (t80) REVERT: G 58 GLU cc_start: 0.7796 (tm-30) cc_final: 0.7453 (tm-30) REVERT: G 62 ARG cc_start: 0.5521 (ptp90) cc_final: 0.5177 (ptp90) REVERT: R 25 PHE cc_start: 0.7290 (t80) cc_final: 0.6628 (t80) REVERT: R 118 MET cc_start: 0.5640 (OUTLIER) cc_final: 0.5259 (mtp) REVERT: R 137 MET cc_start: 0.5948 (tmm) cc_final: 0.5668 (tmm) REVERT: R 215 ASN cc_start: 0.7731 (m-40) cc_final: 0.7078 (m-40) outliers start: 39 outliers final: 28 residues processed: 162 average time/residue: 0.2348 time to fit residues: 51.4057 Evaluate side-chains 152 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 136 THR 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 234 PHE 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 N residue 30 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 163 SER 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 118 MET Chi-restraints excluded: chain R residue 161 LEU Chi-restraints excluded: chain R residue 217 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: 0.4980 chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 0.0040 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 61 optimal weight: 0.1980 chunk 109 optimal weight: 0.2980 chunk 68 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 overall best weight: 0.3392 ------------------------------------------------------------------------------- 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: 0.6352 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9218 Z= 0.131 Angle : 0.534 11.002 12502 Z= 0.268 Chirality : 0.041 0.311 1438 Planarity : 0.004 0.057 1589 Dihedral : 4.433 58.523 1274 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.98 % Allowed : 20.43 % Favored : 76.59 % 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: 0.20 (0.26), residues: 1141 helix: 1.69 (0.27), residues: 389 sheet: -0.29 (0.32), residues: 280 loop : -0.89 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 211 HIS 0.003 0.001 HIS R 112 PHE 0.014 0.001 PHE R 303 TYR 0.010 0.001 TYR N 236 ARG 0.008 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 166 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 137 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 SER cc_start: 0.7955 (t) cc_final: 0.7508 (t) REVERT: B 197 ARG cc_start: 0.7143 (mmt180) cc_final: 0.6758 (mmt180) REVERT: B 214 ARG cc_start: 0.7460 (mpt180) cc_final: 0.6884 (ttp80) REVERT: B 233 CYS cc_start: 0.7847 (t) cc_final: 0.7602 (t) REVERT: N 161 ARG cc_start: 0.7266 (ttp-110) cc_final: 0.6877 (mtm110) REVERT: N 236 TYR cc_start: 0.4735 (OUTLIER) cc_final: 0.4149 (t80) REVERT: G 62 ARG cc_start: 0.5496 (ptp90) cc_final: 0.5140 (ptp90) REVERT: R 25 PHE cc_start: 0.7354 (t80) cc_final: 0.6666 (t80) REVERT: R 118 MET cc_start: 0.5644 (OUTLIER) cc_final: 0.5313 (mtp) REVERT: R 137 MET cc_start: 0.5856 (tmm) cc_final: 0.5650 (tmm) REVERT: R 196 LEU cc_start: 0.6897 (mt) cc_final: 0.6449 (pt) REVERT: R 215 ASN cc_start: 0.7636 (m-40) cc_final: 0.6992 (m-40) outliers start: 29 outliers final: 22 residues processed: 161 average time/residue: 0.2167 time to fit residues: 47.8990 Evaluate side-chains 153 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 129 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 122 LEU 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 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 30 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 227 VAL Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 118 MET 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: 5.9990 chunk 65 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 69 optimal weight: 3.9990 chunk 74 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 99 optimal weight: 0.9990 chunk 105 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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: 0.6411 moved from start: 0.3098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9218 Z= 0.231 Angle : 0.578 11.048 12502 Z= 0.292 Chirality : 0.043 0.272 1438 Planarity : 0.004 0.052 1589 Dihedral : 4.647 58.352 1274 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.18 % Allowed : 20.43 % Favored : 76.39 % 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: 0.19 (0.26), residues: 1141 helix: 1.65 (0.27), residues: 389 sheet: -0.28 (0.32), residues: 280 loop : -0.87 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.007 0.001 HIS B 142 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR N 236 ARG 0.008 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 159 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 128 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7623 (m-80) cc_final: 0.6789 (m-80) REVERT: B 197 ARG cc_start: 0.7124 (mmt180) cc_final: 0.6655 (mmt180) REVERT: B 214 ARG cc_start: 0.7530 (mpt180) cc_final: 0.6906 (ttp80) REVERT: B 304 ARG cc_start: 0.8202 (ttm170) cc_final: 0.7550 (ttm110) REVERT: N 82 GLN cc_start: 0.7085 (tp40) cc_final: 0.6876 (tp40) REVERT: N 161 ARG cc_start: 0.7228 (ttp-110) cc_final: 0.6828 (mtm110) REVERT: G 58 GLU cc_start: 0.7713 (tm-30) cc_final: 0.7425 (tm-30) REVERT: G 62 ARG cc_start: 0.5874 (ptp90) cc_final: 0.5506 (ptp90) REVERT: R 25 PHE cc_start: 0.7294 (t80) cc_final: 0.6633 (t80) REVERT: R 118 MET cc_start: 0.5702 (OUTLIER) cc_final: 0.5332 (mtp) REVERT: R 215 ASN cc_start: 0.7730 (m-40) cc_final: 0.7095 (m-40) outliers start: 31 outliers final: 28 residues processed: 154 average time/residue: 0.2219 time to fit residues: 46.8126 Evaluate side-chains 154 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 0.906 ------------------------------------------------------------------------------- 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 122 LEU 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 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE 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 277 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 200 VAL Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 118 MET 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: 1.9990 chunk 105 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 80 optimal weight: 5.9990 chunk 31 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 chunk 67 optimal weight: 0.9980 chunk 108 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 ** R 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6386 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9218 Z= 0.169 Angle : 0.550 11.166 12502 Z= 0.276 Chirality : 0.041 0.251 1438 Planarity : 0.004 0.057 1589 Dihedral : 4.513 56.182 1274 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.29 % Allowed : 20.43 % Favored : 76.28 % 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: 0.26 (0.26), residues: 1141 helix: 1.74 (0.27), residues: 389 sheet: -0.31 (0.32), residues: 282 loop : -0.80 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.012 0.001 PHE R 303 TYR 0.011 0.001 TYR N 236 ARG 0.006 0.000 ARG B 96 *********************** 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 161 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7564 (m-80) cc_final: 0.6745 (m-80) REVERT: B 197 ARG cc_start: 0.7130 (mmt180) cc_final: 0.6720 (mmt180) REVERT: B 214 ARG cc_start: 0.7532 (mpt180) cc_final: 0.6902 (ttp80) REVERT: B 304 ARG cc_start: 0.8177 (ttm170) cc_final: 0.7892 (ttp-170) REVERT: N 82 GLN cc_start: 0.7116 (tp40) cc_final: 0.6909 (tp40) REVERT: N 161 ARG cc_start: 0.7244 (ttp-110) cc_final: 0.6851 (mtm110) REVERT: N 236 TYR cc_start: 0.4857 (OUTLIER) cc_final: 0.4207 (t80) REVERT: G 62 ARG cc_start: 0.6016 (ptp90) cc_final: 0.5655 (ptp90) REVERT: R 25 PHE cc_start: 0.7302 (t80) cc_final: 0.6589 (t80) REVERT: R 118 MET cc_start: 0.5679 (OUTLIER) cc_final: 0.5319 (mtp) REVERT: R 177 PHE cc_start: 0.6680 (t80) cc_final: 0.6392 (t80) REVERT: R 215 ASN cc_start: 0.7631 (m-40) cc_final: 0.7031 (m-40) outliers start: 32 outliers final: 27 residues processed: 156 average time/residue: 0.2286 time to fit residues: 49.0078 Evaluate side-chains 155 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 126 time to evaluate : 1.058 ------------------------------------------------------------------------------- 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 122 LEU Chi-restraints excluded: chain A residue 136 THR 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 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain N residue 30 SER Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 87 ARG Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 97 VAL Chi-restraints excluded: chain N residue 120 SER Chi-restraints excluded: chain N residue 194 SER Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain N residue 236 TYR Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 118 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 51 optimal weight: 0.7980 chunk 75 optimal weight: 6.9990 chunk 113 optimal weight: 0.0770 chunk 104 optimal weight: 2.9990 chunk 90 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.5136 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.3322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 9218 Z= 0.148 Angle : 0.544 11.161 12502 Z= 0.273 Chirality : 0.041 0.240 1438 Planarity : 0.004 0.054 1589 Dihedral : 4.354 55.246 1274 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 3.29 % Allowed : 20.64 % Favored : 76.08 % 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 (0.26), residues: 1141 helix: 1.83 (0.27), residues: 390 sheet: -0.28 (0.32), residues: 278 loop : -0.74 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 211 HIS 0.004 0.001 HIS B 142 PHE 0.011 0.001 PHE R 303 TYR 0.010 0.001 TYR N 236 ARG 0.007 0.000 ARG B 96 ********************** 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 164 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 132 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 TYR cc_start: 0.7560 (m-80) cc_final: 0.6705 (m-80) REVERT: B 197 ARG cc_start: 0.7117 (mmt180) cc_final: 0.6747 (mmt180) REVERT: B 214 ARG cc_start: 0.7550 (mpt180) cc_final: 0.6916 (ttp80) REVERT: B 233 CYS cc_start: 0.7962 (t) cc_final: 0.7716 (t) REVERT: N 82 GLN cc_start: 0.7078 (tp40) cc_final: 0.6871 (tp40) REVERT: N 161 ARG cc_start: 0.7257 (ttp-110) cc_final: 0.6833 (mtm110) REVERT: G 62 ARG cc_start: 0.6277 (ptp90) cc_final: 0.5926 (ptp90) REVERT: R 25 PHE cc_start: 0.7367 (t80) cc_final: 0.6719 (t80) REVERT: R 118 MET cc_start: 0.5685 (OUTLIER) cc_final: 0.5357 (mtp) REVERT: R 177 PHE cc_start: 0.6706 (t80) cc_final: 0.6393 (t80) REVERT: R 215 ASN cc_start: 0.7602 (m-40) cc_final: 0.7008 (m-40) outliers start: 32 outliers final: 27 residues processed: 158 average time/residue: 0.2211 time to fit residues: 48.0740 Evaluate side-chains 154 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 126 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 122 LEU 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 184 THR Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 234 PHE 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 277 SER Chi-restraints excluded: chain N residue 30 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 194 SER Chi-restraints excluded: chain N residue 227 VAL Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain R residue 64 LEU Chi-restraints excluded: chain R residue 118 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 83 optimal weight: 0.2980 chunk 13 optimal weight: 0.4980 chunk 25 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 143 GLN R 290 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.169738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.112384 restraints weight = 10112.330| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.88 r_work: 0.3128 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 9218 Z= 0.374 Angle : 0.659 12.639 12502 Z= 0.335 Chirality : 0.046 0.248 1438 Planarity : 0.004 0.056 1589 Dihedral : 4.921 55.102 1274 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.49 % Allowed : 20.84 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1141 helix: 1.56 (0.26), residues: 388 sheet: -0.61 (0.31), residues: 295 loop : -0.72 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 211 HIS 0.006 0.001 HIS B 142 PHE 0.016 0.002 PHE G 61 TYR 0.018 0.002 TYR N 236 ARG 0.008 0.001 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2165.36 seconds wall clock time: 39 minutes 26.97 seconds (2366.97 seconds total)