Starting phenix.real_space_refine on Mon Mar 11 06:06:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdc_29946/03_2024/8gdc_29946_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdc_29946/03_2024/8gdc_29946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdc_29946/03_2024/8gdc_29946.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdc_29946/03_2024/8gdc_29946.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdc_29946/03_2024/8gdc_29946_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gdc_29946/03_2024/8gdc_29946_neut_updated.pdb" } resolution = 3.5 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= 0.002 sd= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1646 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 3631 2.51 5 N 966 2.21 5 O 1020 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A GLU 276": "OE1" <-> "OE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "R GLU 154": "OE1" <-> "OE2" Residue "R ARG 155": "NH1" <-> "NH2" Residue "R ARG 350": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5657 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1457 Classifications: {'peptide': 207} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 2, 'TRANS': 204} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 224 Unresolved non-hydrogen angles: 268 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 7, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 108 Chain: "B" Number of atoms: 2174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 310, 2174 Classifications: {'peptide': 310} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 60} Link IDs: {'PTRANS': 5, 'TRANS': 304} Unresolved non-hydrogen bonds: 205 Unresolved non-hydrogen angles: 256 Unresolved non-hydrogen dihedrals: 158 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 14, 'ASN:plan1': 5, 'HIS:plan': 2, 'GLU:plan': 4, 'ARG:plan': 10} Unresolved non-hydrogen planarities: 145 Chain: "C" Number of atoms: 213 Number of conformers: 1 Conformer: "" Number of residues, atoms: 35, 213 Classifications: {'peptide': 35} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 4, 'TRANS': 30} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 46 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 29 Chain: "R" Number of atoms: 1788 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 258, 1781 Classifications: {'peptide': 258} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 65} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 Conformer: "B" Number of residues, atoms: 258, 1781 Classifications: {'peptide': 258} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 65} Link IDs: {'PTRANS': 8, 'TRANS': 249} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 294 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 2, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 1, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 83 bond proxies already assigned to first conformer: 1808 Chain: "R" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 25 Unusual residues: {'P2E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.72, per 1000 atoms: 0.83 Number of scatterers: 5657 At special positions: 0 Unit cell: (84.15, 93.5, 108.8, 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 40 16.00 O 1020 8.00 N 966 7.00 C 3631 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 130 " - pdb=" SG CYS R 208 " 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: 2.14 Conformation dependent library (CDL) restraints added in 1.5 seconds 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 10 sheets defined 37.0% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'A' and resid 7 through 32 removed outlier: 3.969A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 52 Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.718A pdb=" N ILE A 212 " --> pdb=" O ARG A 208 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) removed outlier: 5.912A pdb=" N CYS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE A 215 " --> pdb=" O TRP A 211 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 208 through 215' Processing helix chain 'A' and resid 244 through 254 Processing helix chain 'A' and resid 272 through 280 Processing helix chain 'A' and resid 296 through 310 removed outlier: 4.160A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 339 Processing helix chain 'A' and resid 342 through 350 Processing helix chain 'B' and resid 33 through 36 removed outlier: 4.101A pdb=" N ASN B 36 " --> pdb=" O ILE B 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 33 through 36' Processing helix chain 'C' and resid 30 through 42 Processing helix chain 'R' and resid 53 through 75 removed outlier: 4.227A pdb=" N LEU R 68 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA R 69 " --> pdb=" O GLY R 65 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N MET R 70 " --> pdb=" O ASN R 66 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ARG R 75 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 104 removed outlier: 4.101A pdb=" N LEU R 95 " --> pdb=" O CYS R 91 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR R 98 " --> pdb=" O TRP R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 116 removed outlier: 3.695A pdb=" N LEU R 115 " --> pdb=" O ILE R 111 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N SER R 116 " --> pdb=" O VAL R 112 " (cutoff:3.500A) Processing helix chain 'R' and resid 120 through 123 No H-bonds generated for 'chain 'R' and resid 120 through 123' Processing helix chain 'R' and resid 129 through 160 removed outlier: 3.599A pdb=" N LEU R 135 " --> pdb=" O THR R 131 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET R 137 " --> pdb=" O PHE R 133 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N THR R 138 " --> pdb=" O GLY R 134 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N SER R 144 " --> pdb=" O PHE R 140 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU R 145 " --> pdb=" O GLY R 141 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ALA R 150 " --> pdb=" O PHE R 146 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N MET R 151 " --> pdb=" O ILE R 147 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE R 159 " --> pdb=" O ARG R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 168 removed outlier: 3.740A pdb=" N HIS R 168 " --> pdb=" O TRP R 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 164 through 168' Processing helix chain 'R' and resid 181 through 191 removed outlier: 4.378A pdb=" N PHE R 188 " --> pdb=" O ALA R 184 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA R 189 " --> pdb=" O VAL R 185 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N LEU R 191 " --> pdb=" O ALA R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 227 through 261 removed outlier: 4.136A pdb=" N ALA R 241 " --> pdb=" O LEU R 237 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU R 242 " --> pdb=" O GLY R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 273 through 284 Processing helix chain 'R' and resid 286 through 293 removed outlier: 4.057A pdb=" N SER R 292 " --> pdb=" O MET R 288 " (cutoff:3.500A) Processing helix chain 'R' and resid 297 through 306 removed outlier: 3.586A pdb=" N MET R 302 " --> pdb=" O LEU R 298 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU R 303 " --> pdb=" O LEU R 299 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS R 304 " --> pdb=" O ILE R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 327 through 347 removed outlier: 3.699A pdb=" N VAL R 332 " --> pdb=" O PHE R 328 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ARG R 333 " --> pdb=" O LEU R 329 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ASN R 338 " --> pdb=" O LEU R 334 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N GLN R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Proline residue: R 343 - end of helix removed outlier: 3.796A pdb=" N TYR R 346 " --> pdb=" O ASP R 342 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU R 347 " --> pdb=" O PRO R 343 " (cutoff:3.500A) Processing helix chain 'R' and resid 349 through 352 No H-bonds generated for 'chain 'R' and resid 349 through 352' Processing sheet with id= A, first strand: chain 'A' and resid 186 through 190 removed outlier: 3.600A pdb=" N PHE A 189 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 223 through 225 Processing sheet with id= C, first strand: chain 'B' and resid 69 through 73 removed outlier: 3.636A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.312A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.999A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 207 through 210 removed outlier: 3.648A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.935A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 275 through 278 removed outlier: 3.795A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 327 through 330 removed outlier: 3.551A pdb=" N VAL B 327 " --> pdb=" O TRP B 339 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.827A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'R' and resid 199 through 201 207 hydrogen bonds defined for protein. 615 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: 1.38 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 919 1.28 - 1.42: 1528 1.42 - 1.55: 3253 1.55 - 1.68: 13 1.68 - 1.82: 54 Bond restraints: 5767 Sorted by residual: bond pdb=" CA ILE R 159 " pdb=" CB ILE R 159 " ideal model delta sigma weight residual 1.540 1.435 0.104 1.29e-02 6.01e+03 6.54e+01 bond pdb=" C PRO R 162 " pdb=" O PRO R 162 " ideal model delta sigma weight residual 1.237 1.152 0.086 1.29e-02 6.01e+03 4.41e+01 bond pdb=" C VAL R 112 " pdb=" O VAL R 112 " ideal model delta sigma weight residual 1.237 1.162 0.074 1.12e-02 7.97e+03 4.41e+01 bond pdb=" C LEU R 347 " pdb=" O LEU R 347 " ideal model delta sigma weight residual 1.236 1.180 0.056 8.80e-03 1.29e+04 4.00e+01 bond pdb=" CA ALA R 150 " pdb=" C ALA R 150 " ideal model delta sigma weight residual 1.524 1.442 0.082 1.29e-02 6.01e+03 3.99e+01 ... (remaining 5762 not shown) Histogram of bond angle deviations from ideal: 97.09 - 104.49: 76 104.49 - 111.89: 2676 111.89 - 119.28: 2056 119.28 - 126.68: 2970 126.68 - 134.08: 103 Bond angle restraints: 7881 Sorted by residual: angle pdb=" C ALA R 161 " pdb=" N PRO R 162 " pdb=" CA PRO R 162 " ideal model delta sigma weight residual 119.32 130.23 -10.91 1.14e+00 7.69e-01 9.15e+01 angle pdb=" N ILE R 147 " pdb=" CA ILE R 147 " pdb=" C ILE R 147 " ideal model delta sigma weight residual 112.96 103.95 9.01 1.00e+00 1.00e+00 8.12e+01 angle pdb=" N SER R 116 " pdb=" CA SER R 116 " pdb=" C SER R 116 " ideal model delta sigma weight residual 111.28 121.04 -9.76 1.09e+00 8.42e-01 8.01e+01 angle pdb=" N HIS R 168 " pdb=" CA HIS R 168 " pdb=" C HIS R 168 " ideal model delta sigma weight residual 112.92 123.81 -10.89 1.23e+00 6.61e-01 7.84e+01 angle pdb=" N ALA R 187 " pdb=" CA ALA R 187 " pdb=" C ALA R 187 " ideal model delta sigma weight residual 112.97 103.65 9.32 1.06e+00 8.90e-01 7.74e+01 ... (remaining 7876 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.68: 3028 16.68 - 33.37: 239 33.37 - 50.05: 49 50.05 - 66.74: 5 66.74 - 83.42: 3 Dihedral angle restraints: 3324 sinusoidal: 994 harmonic: 2330 Sorted by residual: dihedral pdb=" C TYR R 114 " pdb=" N TYR R 114 " pdb=" CA TYR R 114 " pdb=" CB TYR R 114 " ideal model delta harmonic sigma weight residual -122.60 -162.91 40.31 0 2.50e+00 1.60e-01 2.60e+02 dihedral pdb=" N TYR R 114 " pdb=" C TYR R 114 " pdb=" CA TYR R 114 " pdb=" CB TYR R 114 " ideal model delta harmonic sigma weight residual 122.80 163.01 -40.21 0 2.50e+00 1.60e-01 2.59e+02 dihedral pdb=" C TYR R 165 " pdb=" N TYR R 165 " pdb=" CA TYR R 165 " pdb=" CB TYR R 165 " ideal model delta harmonic sigma weight residual -122.60 -144.10 21.50 0 2.50e+00 1.60e-01 7.39e+01 ... (remaining 3321 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.360: 942 0.360 - 0.719: 12 0.719 - 1.079: 2 1.079 - 1.438: 0 1.438 - 1.798: 1 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA TYR R 114 " pdb=" N TYR R 114 " pdb=" C TYR R 114 " pdb=" CB TYR R 114 " both_signs ideal model delta sigma weight residual False 2.51 0.71 1.80 2.00e-01 2.50e+01 8.08e+01 chirality pdb=" CA ASN R 249 " pdb=" N ASN R 249 " pdb=" C ASN R 249 " pdb=" CB ASN R 249 " both_signs ideal model delta sigma weight residual False 2.51 1.49 1.02 2.00e-01 2.50e+01 2.60e+01 chirality pdb=" CA TYR R 165 " pdb=" N TYR R 165 " pdb=" C TYR R 165 " pdb=" CB TYR R 165 " both_signs ideal model delta sigma weight residual False 2.51 1.56 0.95 2.00e-01 2.50e+01 2.26e+01 ... (remaining 954 not shown) Planarity restraints: 999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 P2E R 401 " -0.085 2.00e-02 2.50e+03 1.98e-01 3.93e+02 pdb=" C5 P2E R 401 " 0.251 2.00e-02 2.50e+03 pdb=" C6 P2E R 401 " -0.274 2.00e-02 2.50e+03 pdb=" C7 P2E R 401 " 0.108 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 P2E R 401 " 0.168 2.00e-02 2.50e+03 1.76e-01 3.11e+02 pdb=" C13 P2E R 401 " -0.149 2.00e-02 2.50e+03 pdb=" C14 P2E R 401 " -0.202 2.00e-02 2.50e+03 pdb=" C15 P2E R 401 " 0.183 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 238 " -0.024 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C GLY R 238 " 0.085 2.00e-02 2.50e+03 pdb=" O GLY R 238 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU R 239 " -0.029 2.00e-02 2.50e+03 ... (remaining 996 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1711 2.81 - 3.33: 4976 3.33 - 3.86: 8618 3.86 - 4.38: 9473 4.38 - 4.90: 16958 Nonbonded interactions: 41736 Sorted by model distance: nonbonded pdb=" OG SER B 122 " pdb=" OE1 GLU B 138 " model vdw 2.289 2.440 nonbonded pdb=" OG SER B 108 " pdb=" OD1 ASN B 110 " model vdw 2.319 2.440 nonbonded pdb=" O ASN A 269 " pdb=" OG1 THR A 324 " model vdw 2.324 2.440 nonbonded pdb=" OG1 THR B 143 " pdb=" OD2 ASP B 163 " model vdw 2.325 2.440 nonbonded pdb=" N LEU R 284 " pdb=" N MET R 285 " model vdw 2.373 2.560 ... (remaining 41731 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.010 Extract box with map and model: 1.950 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 21.270 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6462 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 : 0.012 0.104 5767 Z= 0.783 Angle : 1.459 13.227 7881 Z= 0.943 Chirality : 0.122 1.798 957 Planarity : 0.012 0.198 999 Dihedral : 13.132 83.419 1807 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.62 % Allowed : 4.34 % Favored : 95.04 % Cbeta Deviations : 1.32 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.27), residues: 787 helix: -1.68 (0.27), residues: 300 sheet: -2.44 (0.39), residues: 161 loop : -2.97 (0.30), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP R 164 HIS 0.011 0.003 HIS R 168 PHE 0.027 0.003 PHE B 234 TYR 0.040 0.004 TYR R 114 ARG 0.006 0.001 ARG R 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.647 Fit side-chains REVERT: B 246 ASP cc_start: 0.8607 (t0) cc_final: 0.8346 (t70) REVERT: B 300 LEU cc_start: 0.7936 (tp) cc_final: 0.7720 (tt) outliers start: 3 outliers final: 3 residues processed: 89 average time/residue: 0.1776 time to fit residues: 20.8586 Evaluate side-chains 83 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 80 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 103 GLN Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 333 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 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 213 HIS R 103 GLN R 163 HIS A R 168 HIS ** R 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5767 Z= 0.205 Angle : 0.621 9.609 7881 Z= 0.320 Chirality : 0.043 0.238 957 Planarity : 0.004 0.045 999 Dihedral : 6.296 43.048 876 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.65 % Allowed : 10.95 % Favored : 87.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.31 (0.29), residues: 787 helix: -0.11 (0.29), residues: 319 sheet: -1.70 (0.43), residues: 138 loop : -2.91 (0.29), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 207 HIS 0.004 0.001 HIS B 225 PHE 0.014 0.002 PHE B 234 TYR 0.017 0.002 TYR B 105 ARG 0.002 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.539 Fit side-chains REVERT: A 196 PHE cc_start: 0.8004 (OUTLIER) cc_final: 0.7660 (p90) REVERT: B 95 LEU cc_start: 0.6808 (mt) cc_final: 0.6454 (mt) REVERT: B 300 LEU cc_start: 0.7805 (tp) cc_final: 0.7598 (tt) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 0.1621 time to fit residues: 17.5730 Evaluate side-chains 75 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 0.0270 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 57 optimal weight: 0.0970 chunk 54 optimal weight: 7.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 339 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5767 Z= 0.148 Angle : 0.527 9.482 7881 Z= 0.270 Chirality : 0.041 0.179 957 Planarity : 0.003 0.042 999 Dihedral : 5.088 39.320 869 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.03 % Allowed : 13.02 % Favored : 85.95 % 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: -1.65 (0.30), residues: 787 helix: 0.67 (0.31), residues: 310 sheet: -1.66 (0.42), residues: 150 loop : -2.59 (0.30), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 63 HIS 0.003 0.001 HIS B 225 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR B 124 ARG 0.001 0.000 ARG R 155 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.591 Fit side-chains REVERT: B 95 LEU cc_start: 0.6732 (mt) cc_final: 0.6356 (mt) REVERT: B 188 MET cc_start: 0.6668 (tpp) cc_final: 0.5937 (mmt) REVERT: B 229 ILE cc_start: 0.7343 (mm) cc_final: 0.6971 (mt) REVERT: B 300 LEU cc_start: 0.7737 (tp) cc_final: 0.7522 (tt) outliers start: 5 outliers final: 3 residues processed: 78 average time/residue: 0.1568 time to fit residues: 16.8176 Evaluate side-chains 76 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 76 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 1 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6515 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5767 Z= 0.181 Angle : 0.526 8.939 7881 Z= 0.271 Chirality : 0.042 0.151 957 Planarity : 0.003 0.039 999 Dihedral : 5.013 38.936 869 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.69 % Allowed : 13.22 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.30), residues: 787 helix: 0.66 (0.30), residues: 336 sheet: -1.49 (0.41), residues: 156 loop : -2.57 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 273 HIS 0.003 0.001 HIS B 225 PHE 0.013 0.002 PHE B 241 TYR 0.013 0.001 TYR B 105 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.603 Fit side-chains REVERT: B 188 MET cc_start: 0.6675 (tpp) cc_final: 0.6003 (mmt) REVERT: B 229 ILE cc_start: 0.7338 (mm) cc_final: 0.6998 (mt) REVERT: B 300 LEU cc_start: 0.7711 (tp) cc_final: 0.7496 (tt) REVERT: R 295 TRP cc_start: 0.7848 (m100) cc_final: 0.7518 (m100) outliers start: 13 outliers final: 11 residues processed: 82 average time/residue: 0.1574 time to fit residues: 17.4695 Evaluate side-chains 84 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 256 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 0.0070 chunk 68 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5767 Z= 0.148 Angle : 0.486 9.421 7881 Z= 0.248 Chirality : 0.041 0.139 957 Planarity : 0.003 0.038 999 Dihedral : 4.737 37.065 869 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.89 % Allowed : 15.50 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.30), residues: 787 helix: 0.88 (0.30), residues: 336 sheet: -1.22 (0.41), residues: 156 loop : -2.42 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 82 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR B 105 ARG 0.002 0.000 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.584 Fit side-chains REVERT: A 196 PHE cc_start: 0.7998 (OUTLIER) cc_final: 0.7109 (p90) REVERT: B 102 THR cc_start: 0.6950 (t) cc_final: 0.6474 (m) REVERT: B 188 MET cc_start: 0.6562 (tpp) cc_final: 0.6273 (mmm) REVERT: B 300 LEU cc_start: 0.7626 (tp) cc_final: 0.7415 (tt) REVERT: R 295 TRP cc_start: 0.7796 (m100) cc_final: 0.7469 (m100) outliers start: 14 outliers final: 10 residues processed: 83 average time/residue: 0.1442 time to fit residues: 16.5855 Evaluate side-chains 82 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.0000 chunk 6 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 73 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 55 optimal weight: 10.0000 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6494 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5767 Z= 0.150 Angle : 0.481 8.822 7881 Z= 0.246 Chirality : 0.040 0.138 957 Planarity : 0.003 0.037 999 Dihedral : 4.615 35.553 869 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.89 % Allowed : 18.18 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.31), residues: 787 helix: 1.00 (0.30), residues: 336 sheet: -1.33 (0.40), residues: 168 loop : -2.30 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 273 HIS 0.002 0.001 HIS B 225 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR B 105 ARG 0.001 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 74 time to evaluate : 0.604 Fit side-chains REVERT: A 196 PHE cc_start: 0.7974 (OUTLIER) cc_final: 0.7076 (p90) REVERT: B 138 GLU cc_start: 0.6043 (mm-30) cc_final: 0.5701 (mm-30) REVERT: B 188 MET cc_start: 0.6558 (tpp) cc_final: 0.6258 (mmm) REVERT: B 300 LEU cc_start: 0.7640 (tp) cc_final: 0.7407 (tt) REVERT: R 295 TRP cc_start: 0.7787 (m100) cc_final: 0.7440 (m100) outliers start: 14 outliers final: 10 residues processed: 81 average time/residue: 0.1459 time to fit residues: 16.7274 Evaluate side-chains 83 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 0.0000 chunk 76 optimal weight: 0.7980 chunk 47 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 0.0020 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 54 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5767 Z= 0.163 Angle : 0.483 8.327 7881 Z= 0.249 Chirality : 0.041 0.141 957 Planarity : 0.003 0.039 999 Dihedral : 4.596 36.886 869 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.89 % Allowed : 19.21 % Favored : 77.89 % 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: -0.92 (0.31), residues: 787 helix: 1.05 (0.30), residues: 335 sheet: -1.21 (0.40), residues: 169 loop : -2.25 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 273 HIS 0.002 0.001 HIS B 142 PHE 0.011 0.001 PHE B 241 TYR 0.010 0.001 TYR B 105 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 80 time to evaluate : 0.631 Fit side-chains REVERT: A 196 PHE cc_start: 0.7981 (OUTLIER) cc_final: 0.7626 (p90) REVERT: B 138 GLU cc_start: 0.6045 (mm-30) cc_final: 0.5686 (mm-30) REVERT: B 188 MET cc_start: 0.6521 (tpp) cc_final: 0.6191 (mmm) REVERT: B 229 ILE cc_start: 0.7323 (mm) cc_final: 0.7037 (mt) REVERT: B 291 ASP cc_start: 0.6383 (p0) cc_final: 0.6097 (p0) REVERT: R 295 TRP cc_start: 0.7774 (m100) cc_final: 0.7449 (m100) outliers start: 14 outliers final: 10 residues processed: 87 average time/residue: 0.1351 time to fit residues: 16.8812 Evaluate side-chains 91 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 4.9990 chunk 72 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 42 optimal weight: 0.0040 overall best weight: 1.3796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6557 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5767 Z= 0.268 Angle : 0.550 7.501 7881 Z= 0.287 Chirality : 0.043 0.167 957 Planarity : 0.003 0.038 999 Dihedral : 4.937 38.246 869 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 3.51 % Allowed : 20.25 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.31), residues: 787 helix: 0.89 (0.30), residues: 334 sheet: -1.15 (0.41), residues: 165 loop : -2.30 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 273 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.002 PHE B 199 TYR 0.015 0.002 TYR B 105 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 0.551 Fit side-chains REVERT: A 196 PHE cc_start: 0.8166 (OUTLIER) cc_final: 0.7026 (p90) REVERT: B 188 MET cc_start: 0.6676 (tpp) cc_final: 0.6040 (mmt) REVERT: R 295 TRP cc_start: 0.7871 (m100) cc_final: 0.7520 (m100) outliers start: 17 outliers final: 13 residues processed: 81 average time/residue: 0.1432 time to fit residues: 16.1369 Evaluate side-chains 81 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 181 VAL Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.9990 chunk 55 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 64 optimal weight: 0.8980 chunk 67 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6520 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5767 Z= 0.179 Angle : 0.510 7.619 7881 Z= 0.261 Chirality : 0.041 0.144 957 Planarity : 0.003 0.038 999 Dihedral : 4.630 35.701 869 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.69 % Allowed : 21.07 % Favored : 76.24 % 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: -0.81 (0.31), residues: 787 helix: 1.21 (0.31), residues: 328 sheet: -1.24 (0.40), residues: 172 loop : -2.14 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 273 HIS 0.002 0.001 HIS B 225 PHE 0.013 0.002 PHE B 278 TYR 0.010 0.001 TYR B 105 ARG 0.001 0.000 ARG B 150 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.598 Fit side-chains REVERT: A 196 PHE cc_start: 0.8075 (OUTLIER) cc_final: 0.6978 (p90) REVERT: B 188 MET cc_start: 0.6617 (tpp) cc_final: 0.6048 (mmt) REVERT: R 295 TRP cc_start: 0.7766 (m100) cc_final: 0.7476 (m100) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.1392 time to fit residues: 15.8780 Evaluate side-chains 78 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 72 SER Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 9 optimal weight: 0.0060 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6492 moved from start: 0.4550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5767 Z= 0.142 Angle : 0.488 7.402 7881 Z= 0.249 Chirality : 0.041 0.135 957 Planarity : 0.003 0.039 999 Dihedral : 4.350 33.047 869 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.69 % Allowed : 21.90 % Favored : 75.41 % 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: -0.57 (0.31), residues: 787 helix: 1.45 (0.31), residues: 329 sheet: -1.07 (0.41), residues: 170 loop : -2.10 (0.33), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 273 HIS 0.002 0.001 HIS R 168 PHE 0.011 0.001 PHE B 278 TYR 0.008 0.001 TYR B 105 ARG 0.001 0.000 ARG B 150 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1574 Ramachandran restraints generated. 787 Oldfield, 0 Emsley, 787 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.559 Fit side-chains REVERT: A 20 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6495 (t70) REVERT: A 196 PHE cc_start: 0.8025 (OUTLIER) cc_final: 0.7024 (p90) REVERT: B 61 MET cc_start: 0.5433 (ppp) cc_final: 0.5210 (ppp) REVERT: B 138 GLU cc_start: 0.6004 (mm-30) cc_final: 0.5650 (mm-30) REVERT: B 188 MET cc_start: 0.6548 (tpp) cc_final: 0.5989 (mmt) REVERT: R 295 TRP cc_start: 0.7705 (m100) cc_final: 0.7412 (m100) outliers start: 13 outliers final: 11 residues processed: 84 average time/residue: 0.1276 time to fit residues: 15.3658 Evaluate side-chains 87 residues out of total 684 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 196 PHE Chi-restraints excluded: chain B residue 158 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain R residue 114 TYR Chi-restraints excluded: chain R residue 137 MET Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 209 PHE Chi-restraints excluded: chain R residue 243 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.0970 chunk 62 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 64 optimal weight: 0.0170 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 71 optimal weight: 0.5980 chunk 42 optimal weight: 2.9990 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 311 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.175570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.153244 restraints weight = 13917.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.156374 restraints weight = 8588.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.159169 restraints weight = 5851.552| |-----------------------------------------------------------------------------| r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4020 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4020 r_free = 0.4020 target_work(ls_wunit_k1) = 0.158 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.4020 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.4642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5767 Z= 0.129 Angle : 0.479 7.161 7881 Z= 0.244 Chirality : 0.040 0.130 957 Planarity : 0.003 0.039 999 Dihedral : 4.180 32.068 869 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.27 % Allowed : 23.14 % Favored : 74.59 % 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: -0.30 (0.32), residues: 787 helix: 1.70 (0.31), residues: 328 sheet: -0.99 (0.41), residues: 177 loop : -1.96 (0.34), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP R 273 HIS 0.002 0.001 HIS R 168 PHE 0.010 0.001 PHE A 189 TYR 0.009 0.001 TYR B 124 ARG 0.002 0.000 ARG B 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1396.65 seconds wall clock time: 26 minutes 13.11 seconds (1573.11 seconds total)