Starting phenix.real_space_refine on Fri Feb 16 02:05:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn4_27554/02_2024/8dn4_27554_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn4_27554/02_2024/8dn4_27554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn4_27554/02_2024/8dn4_27554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn4_27554/02_2024/8dn4_27554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn4_27554/02_2024/8dn4_27554_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn4_27554/02_2024/8dn4_27554_trim_updated.pdb" } resolution = 4.1 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= 0.010 sd= 0.062 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 100 5.16 5 C 9031 2.51 5 N 2234 2.21 5 O 2452 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13817 Number of models: 1 Model: "" Number of chains: 10 Chain: "D" Number of atoms: 2770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2770 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "A" Number of atoms: 2723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2723 Classifications: {'peptide': 335} Link IDs: {'PTRANS': 15, 'TRANS': 319} Chain breaks: 1 Chain: "B" Number of atoms: 2745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2745 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 2728 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 2728 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 15, 'TRANS': 321} Chain breaks: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "E" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2693 Classifications: {'peptide': 332} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 315} Chain breaks: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 35 Unusual residues: {'HEX': 2, 'LNK': 1, 'NAG': 1, 'NBU': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 40 Unusual residues: {'HEX': 3, 'NAG': 1, 'OCT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 26 Unusual residues: {'HEX': 2, 'NAG': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 37 Unusual residues: {'DD9': 1, 'HEX': 1, 'NAG': 1, 'NBU': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 20 Unusual residues: {'HEX': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 8.28, per 1000 atoms: 0.60 Number of scatterers: 13817 At special positions: 0 Unit cell: (101.26, 122.84, 130.31, 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 100 16.00 O 2452 8.00 N 2234 7.00 C 9031 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 152 " distance=2.03 Simple disulfide: pdb=" SG CYS D 198 " - pdb=" SG CYS D 209 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 152 " distance=2.03 Simple disulfide: pdb=" SG CYS A 198 " - pdb=" SG CYS A 209 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 152 " distance=2.03 Simple disulfide: pdb=" SG CYS B 198 " - pdb=" SG CYS B 209 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 152 " distance=2.03 Simple disulfide: pdb=" SG CYS C 198 " - pdb=" SG CYS C 209 " distance=2.04 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.04 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " 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 Links applied NAG-ASN " NAG A 501 " - " ASN A 38 " " NAG B 501 " - " ASN B 38 " " NAG C 501 " - " ASN C 38 " " NAG D 501 " - " ASN D 38 " " NAG E 501 " - " ASN E 220 " Time building additional restraints: 5.57 Conformation dependent library (CDL) restraints added in 2.4 seconds 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3218 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 41 helices and 18 sheets defined 36.6% alpha, 16.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.70 Creating SS restraints... Processing helix chain 'D' and resid 10 through 17 Processing helix chain 'D' and resid 20 through 22 No H-bonds generated for 'chain 'D' and resid 20 through 22' Processing helix chain 'D' and resid 53 through 55 No H-bonds generated for 'chain 'D' and resid 53 through 55' Processing helix chain 'D' and resid 87 through 92 removed outlier: 5.028A pdb=" N ASP D 91 " --> pdb=" O SER D 88 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 147 No H-bonds generated for 'chain 'D' and resid 145 through 147' Processing helix chain 'D' and resid 221 through 243 Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 249 through 273 removed outlier: 4.275A pdb=" N SER D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 284 through 310 Processing helix chain 'D' and resid 386 through 418 Proline residue: D 403 - end of helix Processing helix chain 'A' and resid 10 through 17 Processing helix chain 'A' and resid 20 through 22 No H-bonds generated for 'chain 'A' and resid 20 through 22' Processing helix chain 'A' and resid 71 through 73 No H-bonds generated for 'chain 'A' and resid 71 through 73' Processing helix chain 'A' and resid 87 through 92 removed outlier: 4.671A pdb=" N ASP A 91 " --> pdb=" O SER A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 243 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 249 through 270 Processing helix chain 'A' and resid 283 through 308 Processing helix chain 'A' and resid 388 through 416 Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 71 through 73 No H-bonds generated for 'chain 'B' and resid 71 through 73' Processing helix chain 'B' and resid 87 through 92 removed outlier: 4.016A pdb=" N ASP B 91 " --> pdb=" O SER B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 147 No H-bonds generated for 'chain 'B' and resid 145 through 147' Processing helix chain 'B' and resid 221 through 243 removed outlier: 3.526A pdb=" N ILE B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 249 through 273 removed outlier: 3.581A pdb=" N ALA B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 283 through 308 Processing helix chain 'B' and resid 386 through 417 removed outlier: 4.716A pdb=" N PHE B 402 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Proline residue: B 403 - end of helix Processing helix chain 'C' and resid 10 through 17 Processing helix chain 'C' and resid 20 through 22 No H-bonds generated for 'chain 'C' and resid 20 through 22' Processing helix chain 'C' and resid 71 through 73 No H-bonds generated for 'chain 'C' and resid 71 through 73' Processing helix chain 'C' and resid 87 through 92 removed outlier: 4.058A pdb=" N ASP C 91 " --> pdb=" O SER C 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 221 through 242 Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 246 through 273 Proline residue: C 250 - end of helix Processing helix chain 'C' and resid 283 through 309 Processing helix chain 'C' and resid 387 through 416 Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 35 through 42 Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 110 through 115 Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 252 through 266 Processing helix chain 'E' and resid 276 through 295 Processing helix chain 'E' and resid 306 through 332 Processing helix chain 'E' and resid 448 through 474 Proline residue: E 460 - end of helix Processing sheet with id= A, first strand: chain 'D' and resid 83 through 85 removed outlier: 4.771A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER D 47 " --> pdb=" O ASN D 61 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N PHE D 63 " --> pdb=" O ILE D 45 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ILE D 45 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ARG D 65 " --> pdb=" O ILE D 43 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ILE D 43 " --> pdb=" O ARG D 65 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLN D 67 " --> pdb=" O CYS D 41 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N CYS D 41 " --> pdb=" O GLN D 67 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 98 through 100 removed outlier: 3.695A pdb=" N ALA D 212 " --> pdb=" O MET D 154 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 187 through 189 Processing sheet with id= D, first strand: chain 'A' and resid 132 through 137 removed outlier: 5.775A pdb=" N PHE A 63 " --> pdb=" O ILE A 45 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N ILE A 45 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N ARG A 65 " --> pdb=" O ILE A 43 " (cutoff:3.500A) removed outlier: 5.408A pdb=" N ILE A 43 " --> pdb=" O ARG A 65 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N GLN A 67 " --> pdb=" O CYS A 41 " (cutoff:3.500A) removed outlier: 5.116A pdb=" N CYS A 41 " --> pdb=" O GLN A 67 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 65 through 69 removed outlier: 3.525A pdb=" N TYR A 128 " --> pdb=" O GLN A 66 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 149 through 157 removed outlier: 3.557A pdb=" N ALA A 212 " --> pdb=" O MET A 154 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 166 through 169 removed outlier: 6.273A pdb=" N VAL B 37 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N GLU B 169 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL B 39 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N ASN B 38 " --> pdb=" O ASN B 69 " (cutoff:3.500A) removed outlier: 5.015A pdb=" N ASN B 69 " --> pdb=" O ASN B 38 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N LEU B 118 " --> pdb=" O LEU B 85 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU B 85 " --> pdb=" O LEU B 118 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 57 through 62 Processing sheet with id= I, first strand: chain 'B' and resid 149 through 157 removed outlier: 3.567A pdb=" N CYS B 152 " --> pdb=" O PHE B 214 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA B 212 " --> pdb=" O MET B 154 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG B 196 " --> pdb=" O GLU B 211 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASP B 194 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'B' and resid 200 through 202 removed outlier: 4.001A pdb=" N LYS B 200 " --> pdb=" O PHE B 207 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE B 207 " --> pdb=" O LYS B 200 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 83 through 85 removed outlier: 4.569A pdb=" N LEU C 118 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N PHE C 63 " --> pdb=" O ILE C 45 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N ILE C 45 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ARG C 65 " --> pdb=" O ILE C 43 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE C 43 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN C 67 " --> pdb=" O CYS C 41 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N CYS C 41 " --> pdb=" O GLN C 67 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 149 through 157 removed outlier: 3.722A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ARG C 196 " --> pdb=" O GLU C 211 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'C' and resid 200 through 202 removed outlier: 4.005A pdb=" N LYS C 200 " --> pdb=" O PHE C 207 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 58 through 62 removed outlier: 3.721A pdb=" N VAL E 62 " --> pdb=" O ILE E 192 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 78 through 89 removed outlier: 3.971A pdb=" N ILE E 83 " --> pdb=" O LEU E 155 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU E 85 " --> pdb=" O MET E 153 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER E 152 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 172 through 180 Processing sheet with id= Q, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.711A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 126 through 129 removed outlier: 7.430A pdb=" N THR E 158 " --> pdb=" O LYS E 127 " (cutoff:3.500A) 565 hydrogen bonds defined for protein. 1497 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: 3.73 Time building geometry restraints manager: 5.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2792 1.33 - 1.45: 3462 1.45 - 1.58: 7725 1.58 - 1.70: 1 1.70 - 1.83: 168 Bond restraints: 14148 Sorted by residual: bond pdb=" C1 NAG B 501 " pdb=" O5 NAG B 501 " ideal model delta sigma weight residual 1.406 1.494 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 NAG A 501 " pdb=" O5 NAG A 501 " ideal model delta sigma weight residual 1.406 1.478 -0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" N GLN D 150 " pdb=" CA GLN D 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.25e-02 6.40e+03 8.95e+00 bond pdb=" N CYS D 152 " pdb=" CA CYS D 152 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.21e-02 6.83e+03 8.68e+00 bond pdb=" N ILE D 153 " pdb=" CA ILE D 153 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.27e-02 6.20e+03 8.22e+00 ... (remaining 14143 not shown) Histogram of bond angle deviations from ideal: 97.37 - 104.71: 265 104.71 - 112.05: 6758 112.05 - 119.39: 4779 119.39 - 126.72: 7123 126.72 - 134.06: 219 Bond angle restraints: 19144 Sorted by residual: angle pdb=" N LYS B 418 " pdb=" CA LYS B 418 " pdb=" C LYS B 418 " ideal model delta sigma weight residual 112.94 106.45 6.49 1.41e+00 5.03e-01 2.12e+01 angle pdb=" N LEU E 167 " pdb=" CA LEU E 167 " pdb=" C LEU E 167 " ideal model delta sigma weight residual 111.24 105.41 5.83 1.38e+00 5.25e-01 1.79e+01 angle pdb=" CA PRO B 146 " pdb=" N PRO B 146 " pdb=" CD PRO B 146 " ideal model delta sigma weight residual 112.00 106.63 5.37 1.40e+00 5.10e-01 1.47e+01 angle pdb=" N THR B 113 " pdb=" CA THR B 113 " pdb=" CB THR B 113 " ideal model delta sigma weight residual 111.57 117.45 -5.88 1.68e+00 3.54e-01 1.23e+01 angle pdb=" C LEU E 464 " pdb=" N PHE E 465 " pdb=" CA PHE E 465 " ideal model delta sigma weight residual 120.72 115.10 5.62 1.67e+00 3.59e-01 1.13e+01 ... (remaining 19139 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.60: 8132 24.60 - 49.20: 331 49.20 - 73.80: 28 73.80 - 98.39: 8 98.39 - 122.99: 9 Dihedral angle restraints: 8508 sinusoidal: 3542 harmonic: 4966 Sorted by residual: dihedral pdb=" CB CYS E 161 " pdb=" SG CYS E 161 " pdb=" SG CYS E 175 " pdb=" CB CYS E 175 " ideal model delta sinusoidal sigma weight residual 93.00 45.14 47.86 1 1.00e+01 1.00e-02 3.16e+01 dihedral pdb=" CA CYS B 209 " pdb=" C CYS B 209 " pdb=" N ILE B 210 " pdb=" CA ILE B 210 " ideal model delta harmonic sigma weight residual 180.00 152.25 27.75 0 5.00e+00 4.00e-02 3.08e+01 dihedral pdb=" CB CYS B 198 " pdb=" SG CYS B 198 " pdb=" SG CYS B 209 " pdb=" CB CYS B 209 " ideal model delta sinusoidal sigma weight residual -86.00 -51.22 -34.78 1 1.00e+01 1.00e-02 1.71e+01 ... (remaining 8505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 1946 0.084 - 0.167: 178 0.167 - 0.251: 11 0.251 - 0.335: 1 0.335 - 0.418: 2 Chirality restraints: 2138 Sorted by residual: chirality pdb=" CB ILE D 51 " pdb=" CA ILE D 51 " pdb=" CG1 ILE D 51 " pdb=" CG2 ILE D 51 " both_signs ideal model delta sigma weight residual False 2.64 2.23 0.42 2.00e-01 2.50e+01 4.38e+00 chirality pdb=" C1 NAG B 501 " pdb=" ND2 ASN B 38 " pdb=" C2 NAG B 501 " pdb=" O5 NAG B 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.03 -0.37 2.00e-01 2.50e+01 3.42e+00 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.81e+00 ... (remaining 2135 not shown) Planarity restraints: 2391 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 239 " 0.028 2.00e-02 2.50e+03 2.92e-02 2.13e+01 pdb=" CG TRP B 239 " -0.075 2.00e-02 2.50e+03 pdb=" CD1 TRP B 239 " 0.042 2.00e-02 2.50e+03 pdb=" CD2 TRP B 239 " -0.009 2.00e-02 2.50e+03 pdb=" NE1 TRP B 239 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 239 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 239 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 239 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 239 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP B 239 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 145 " -0.078 5.00e-02 4.00e+02 1.15e-01 2.11e+01 pdb=" N PRO B 146 " 0.198 5.00e-02 4.00e+02 pdb=" CA PRO B 146 " -0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 146 " -0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 196 " -0.015 2.00e-02 2.50e+03 2.99e-02 8.92e+00 pdb=" C ARG B 196 " 0.052 2.00e-02 2.50e+03 pdb=" O ARG B 196 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR B 197 " -0.017 2.00e-02 2.50e+03 ... (remaining 2388 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 3 2.06 - 2.77: 2601 2.77 - 3.48: 20888 3.48 - 4.19: 31982 4.19 - 4.90: 54228 Nonbonded interactions: 109702 Sorted by model distance: nonbonded pdb=" CD2 LEU D 261 " pdb=" CZ PHE E 282 " model vdw 1.353 3.760 nonbonded pdb=" CG LEU D 261 " pdb=" CZ PHE E 282 " model vdw 1.990 3.770 nonbonded pdb=" CG2 THR A 258 " pdb=" CD1 LEU E 285 " model vdw 2.036 3.880 nonbonded pdb=" O SER E 262 " pdb=" OG SER E 265 " model vdw 2.096 2.440 nonbonded pdb=" O VAL B 235 " pdb=" OG SER B 238 " model vdw 2.112 2.440 ... (remaining 109697 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 8 through 251 or (resid 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 through 309 or (resid 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 through 419 or resid 501 \ )) selection = (chain 'B' and (resid 8 through 309 or (resid 387 and (name N or name CA or name \ C or name O or name CB )) or resid 388 through 419 or resid 501)) selection = (chain 'C' and (resid 8 through 309 or resid 387 through 419 or resid 501)) selection = (chain 'D' and (resid 8 through 251 or (resid 252 and (name N or name CA or name \ C or name O or name CB )) or resid 253 through 309 or (resid 387 and (name N or \ name CA or name C or name O or name CB )) or resid 388 through 419 or resid 501 \ )) } 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 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: 3.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.950 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 39.060 Find NCS groups from input model: 0.930 Set up NCS constraints: 0.070 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 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 : 0.004 0.088 14148 Z= 0.237 Angle : 0.723 7.597 19144 Z= 0.378 Chirality : 0.049 0.418 2138 Planarity : 0.005 0.115 2386 Dihedral : 13.547 122.993 5260 Min Nonbonded Distance : 1.353 Molprobity Statistics. All-atom Clashscore : 18.54 Ramachandran Plot: Outliers : 0.30 % Allowed : 5.78 % Favored : 93.92 % Rotamer: Outliers : 0.40 % Allowed : 0.46 % Favored : 99.14 % 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: -0.28 (0.21), residues: 1662 helix: 1.93 (0.22), residues: 578 sheet: -0.82 (0.31), residues: 302 loop : -1.61 (0.22), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.075 0.002 TRP B 239 HIS 0.001 0.001 HIS D 201 PHE 0.035 0.002 PHE D 412 TYR 0.021 0.001 TYR D 413 ARG 0.008 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 421 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 148 ASP cc_start: 0.9001 (t0) cc_final: 0.7855 (t0) REVERT: D 287 MET cc_start: 0.9100 (mmm) cc_final: 0.8812 (mmm) REVERT: D 311 HIS cc_start: 0.6872 (OUTLIER) cc_final: 0.6555 (m90) REVERT: D 404 MET cc_start: 0.8569 (tmm) cc_final: 0.8304 (tmm) REVERT: D 408 ILE cc_start: 0.9260 (tp) cc_final: 0.8953 (tp) REVERT: A 155 GLN cc_start: 0.8607 (mt0) cc_final: 0.8282 (mt0) REVERT: A 186 GLN cc_start: 0.8769 (mt0) cc_final: 0.8551 (mt0) REVERT: A 211 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7889 (mm-30) REVERT: A 217 GLU cc_start: 0.8367 (mp0) cc_final: 0.8012 (mp0) REVERT: A 220 MET cc_start: 0.7656 (pmm) cc_final: 0.7354 (pmm) REVERT: A 274 LEU cc_start: 0.9497 (mp) cc_final: 0.9107 (tt) REVERT: A 287 MET cc_start: 0.9112 (mmm) cc_final: 0.8523 (mmm) REVERT: B 211 GLU cc_start: 0.7716 (pm20) cc_final: 0.7114 (pm20) REVERT: B 220 MET cc_start: 0.8484 (pmm) cc_final: 0.8198 (pmm) REVERT: B 239 TRP cc_start: 0.8157 (m-90) cc_final: 0.6994 (m-90) REVERT: C 90 LEU cc_start: 0.9431 (tp) cc_final: 0.8778 (tp) REVERT: C 97 ASP cc_start: 0.7122 (p0) cc_final: 0.6523 (p0) REVERT: C 98 LEU cc_start: 0.8964 (tp) cc_final: 0.8663 (tp) REVERT: C 103 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7695 (tm-30) REVERT: C 112 THR cc_start: 0.9400 (p) cc_final: 0.9198 (p) REVERT: C 128 TYR cc_start: 0.8988 (t80) cc_final: 0.8745 (t80) REVERT: C 167 ILE cc_start: 0.7644 (tt) cc_final: 0.7314 (tt) REVERT: C 239 TRP cc_start: 0.7449 (m-10) cc_final: 0.6858 (m-10) REVERT: C 411 MET cc_start: 0.7074 (tpt) cc_final: 0.6752 (mmp) REVERT: C 414 TRP cc_start: 0.8813 (m100) cc_final: 0.8599 (m100) REVERT: E 115 CYS cc_start: 0.8812 (t) cc_final: 0.8612 (t) REVERT: E 170 MET cc_start: 0.8276 (mmm) cc_final: 0.8012 (mmm) REVERT: E 173 GLN cc_start: 0.7178 (mm-40) cc_final: 0.6683 (mm110) REVERT: E 176 LYS cc_start: 0.8995 (ptmm) cc_final: 0.8341 (pttt) REVERT: E 314 CYS cc_start: 0.9327 (m) cc_final: 0.9037 (m) REVERT: E 324 GLU cc_start: 0.8080 (pp20) cc_final: 0.7772 (mm-30) outliers start: 6 outliers final: 2 residues processed: 425 average time/residue: 0.2218 time to fit residues: 142.5464 Evaluate side-chains 326 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 323 time to evaluate : 1.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 9.9990 chunk 125 optimal weight: 0.8980 chunk 69 optimal weight: 7.9990 chunk 42 optimal weight: 4.9990 chunk 84 optimal weight: 6.9990 chunk 67 optimal weight: 7.9990 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 150 optimal weight: 7.9990 overall best weight: 3.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 125 ASN ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 107 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14148 Z= 0.308 Angle : 0.681 9.677 19144 Z= 0.352 Chirality : 0.046 0.345 2138 Planarity : 0.005 0.072 2386 Dihedral : 9.596 112.340 1981 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 18.97 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.92 % Favored : 92.90 % Rotamer: Outliers : 0.33 % Allowed : 5.37 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1662 helix: 1.30 (0.22), residues: 582 sheet: -0.86 (0.30), residues: 308 loop : -1.53 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP B 239 HIS 0.006 0.001 HIS C 201 PHE 0.025 0.002 PHE E 282 TYR 0.013 0.001 TYR D 413 ARG 0.007 0.001 ARG B 196 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 363 time to evaluate : 1.679 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 17 LEU cc_start: 0.9318 (tp) cc_final: 0.8625 (tp) REVERT: D 18 MET cc_start: 0.9224 (pmm) cc_final: 0.8754 (pmm) REVERT: D 89 MET cc_start: 0.9385 (mmm) cc_final: 0.8912 (mpp) REVERT: D 149 VAL cc_start: 0.8944 (OUTLIER) cc_final: 0.8689 (p) REVERT: D 287 MET cc_start: 0.9168 (mmm) cc_final: 0.8745 (mmm) REVERT: D 404 MET cc_start: 0.8555 (tmm) cc_final: 0.8261 (tmm) REVERT: D 408 ILE cc_start: 0.9269 (tp) cc_final: 0.8955 (tp) REVERT: D 412 PHE cc_start: 0.8517 (m-80) cc_final: 0.8073 (m-10) REVERT: A 107 HIS cc_start: 0.8555 (p90) cc_final: 0.8001 (p90) REVERT: A 116 LYS cc_start: 0.9322 (mttt) cc_final: 0.8942 (mtpp) REVERT: A 155 GLN cc_start: 0.8485 (mt0) cc_final: 0.8030 (mt0) REVERT: A 211 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7725 (mm-30) REVERT: A 220 MET cc_start: 0.7901 (pmm) cc_final: 0.7509 (pmm) REVERT: A 274 LEU cc_start: 0.9519 (mp) cc_final: 0.9140 (tt) REVERT: A 287 MET cc_start: 0.9196 (mmm) cc_final: 0.8481 (mmm) REVERT: B 17 LEU cc_start: 0.9330 (tp) cc_final: 0.9007 (tp) REVERT: B 66 GLN cc_start: 0.9112 (mp-120) cc_final: 0.8903 (mp10) REVERT: B 97 ASP cc_start: 0.7780 (p0) cc_final: 0.7440 (p0) REVERT: B 110 GLU cc_start: 0.7670 (mt-10) cc_final: 0.7464 (pt0) REVERT: B 211 GLU cc_start: 0.7219 (pm20) cc_final: 0.7017 (pm20) REVERT: B 220 MET cc_start: 0.8465 (pmm) cc_final: 0.8217 (pmm) REVERT: C 17 LEU cc_start: 0.9293 (tp) cc_final: 0.8940 (tp) REVERT: C 18 MET cc_start: 0.8757 (pmm) cc_final: 0.7978 (pmm) REVERT: C 97 ASP cc_start: 0.7567 (p0) cc_final: 0.6902 (p0) REVERT: C 98 LEU cc_start: 0.9009 (tp) cc_final: 0.8734 (tp) REVERT: C 167 ILE cc_start: 0.7846 (tt) cc_final: 0.7452 (tt) REVERT: C 239 TRP cc_start: 0.7793 (m-10) cc_final: 0.7352 (m-10) REVERT: C 404 MET cc_start: 0.8688 (ttt) cc_final: 0.8320 (tpp) REVERT: C 411 MET cc_start: 0.6761 (tpt) cc_final: 0.6452 (mmp) REVERT: C 414 TRP cc_start: 0.8871 (m100) cc_final: 0.8627 (m100) REVERT: E 74 GLU cc_start: 0.8721 (mp0) cc_final: 0.8506 (mp0) REVERT: E 115 CYS cc_start: 0.8846 (t) cc_final: 0.8592 (t) REVERT: E 173 GLN cc_start: 0.7611 (mm-40) cc_final: 0.7183 (mm110) REVERT: E 176 LYS cc_start: 0.9075 (ptmm) cc_final: 0.8405 (pttt) REVERT: E 193 TRP cc_start: 0.8379 (m100) cc_final: 0.8059 (m100) REVERT: E 314 CYS cc_start: 0.9334 (m) cc_final: 0.9062 (m) outliers start: 5 outliers final: 1 residues processed: 366 average time/residue: 0.2175 time to fit residues: 121.9178 Evaluate side-chains 300 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 298 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 5.9990 chunk 125 optimal weight: 2.9990 chunk 102 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 163 optimal weight: 0.4980 chunk 134 optimal weight: 10.0000 chunk 149 optimal weight: 0.0020 chunk 51 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 overall best weight: 2.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 311 HIS ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14148 Z= 0.235 Angle : 0.657 11.027 19144 Z= 0.334 Chirality : 0.046 0.292 2138 Planarity : 0.005 0.060 2386 Dihedral : 8.532 111.054 1981 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.91 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.38 % Favored : 93.44 % Rotamer: Outliers : 0.20 % Allowed : 4.51 % Favored : 95.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.58 (0.21), residues: 1662 helix: 1.32 (0.22), residues: 575 sheet: -0.83 (0.30), residues: 308 loop : -1.53 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 170 HIS 0.006 0.001 HIS C 201 PHE 0.036 0.002 PHE E 282 TYR 0.016 0.001 TYR D 413 ARG 0.004 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 384 time to evaluate : 1.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.9376 (mmm) cc_final: 0.8886 (mpp) REVERT: D 140 MET cc_start: 0.7426 (mmm) cc_final: 0.6902 (mmm) REVERT: D 141 ASP cc_start: 0.8803 (t0) cc_final: 0.8590 (t0) REVERT: D 145 PHE cc_start: 0.9251 (t80) cc_final: 0.9026 (t80) REVERT: D 287 MET cc_start: 0.9145 (mmm) cc_final: 0.8679 (mmm) REVERT: D 311 HIS cc_start: 0.6883 (OUTLIER) cc_final: 0.6472 (m-70) REVERT: D 404 MET cc_start: 0.8456 (tmm) cc_final: 0.8154 (tmm) REVERT: D 408 ILE cc_start: 0.9248 (tp) cc_final: 0.8918 (tp) REVERT: D 412 PHE cc_start: 0.8483 (m-80) cc_final: 0.8213 (m-80) REVERT: A 90 LEU cc_start: 0.9096 (pp) cc_final: 0.8878 (tp) REVERT: A 116 LYS cc_start: 0.9306 (mttt) cc_final: 0.8905 (mtpp) REVERT: A 155 GLN cc_start: 0.8504 (mt0) cc_final: 0.8085 (mt0) REVERT: A 159 PHE cc_start: 0.8809 (t80) cc_final: 0.8528 (t80) REVERT: A 211 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7803 (mm-30) REVERT: A 220 MET cc_start: 0.7876 (pmm) cc_final: 0.7409 (pmm) REVERT: A 274 LEU cc_start: 0.9479 (mp) cc_final: 0.9143 (tt) REVERT: A 287 MET cc_start: 0.9150 (mmm) cc_final: 0.8717 (mmm) REVERT: A 306 PHE cc_start: 0.8708 (t80) cc_final: 0.8349 (t80) REVERT: B 97 ASP cc_start: 0.7932 (p0) cc_final: 0.7380 (p0) REVERT: B 186 GLN cc_start: 0.8395 (pm20) cc_final: 0.7911 (pm20) REVERT: B 211 GLU cc_start: 0.7020 (pm20) cc_final: 0.6773 (pm20) REVERT: B 220 MET cc_start: 0.8448 (pmm) cc_final: 0.8117 (pmm) REVERT: B 235 VAL cc_start: 0.9537 (p) cc_final: 0.8551 (p) REVERT: B 239 TRP cc_start: 0.8306 (m-90) cc_final: 0.6887 (m-90) REVERT: B 263 MET cc_start: 0.9345 (tpt) cc_final: 0.9128 (tpt) REVERT: C 17 LEU cc_start: 0.9266 (tp) cc_final: 0.8923 (tp) REVERT: C 18 MET cc_start: 0.8791 (pmm) cc_final: 0.7993 (pmm) REVERT: C 97 ASP cc_start: 0.7639 (p0) cc_final: 0.6871 (p0) REVERT: C 98 LEU cc_start: 0.8994 (tp) cc_final: 0.8776 (tp) REVERT: C 103 GLU cc_start: 0.8124 (tm-30) cc_final: 0.7271 (tm-30) REVERT: C 167 ILE cc_start: 0.7773 (tt) cc_final: 0.7371 (tt) REVERT: C 404 MET cc_start: 0.8641 (ttt) cc_final: 0.8047 (tpp) REVERT: C 411 MET cc_start: 0.6557 (tpt) cc_final: 0.6223 (mmp) REVERT: C 414 TRP cc_start: 0.8837 (m100) cc_final: 0.8574 (m100) REVERT: E 77 MET cc_start: 0.7964 (tpp) cc_final: 0.7606 (tpp) REVERT: E 115 CYS cc_start: 0.8808 (t) cc_final: 0.8578 (t) REVERT: E 170 MET cc_start: 0.8296 (mmm) cc_final: 0.7920 (mmm) REVERT: E 173 GLN cc_start: 0.7639 (mm-40) cc_final: 0.7078 (mm110) REVERT: E 176 LYS cc_start: 0.9067 (ptmm) cc_final: 0.8267 (ptmt) REVERT: E 465 PHE cc_start: 0.8196 (p90) cc_final: 0.7940 (p90) outliers start: 3 outliers final: 0 residues processed: 386 average time/residue: 0.2128 time to fit residues: 125.2870 Evaluate side-chains 306 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 305 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 149 optimal weight: 0.4980 chunk 113 optimal weight: 4.9990 chunk 78 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 chunk 151 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 43 optimal weight: 6.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 14148 Z= 0.286 Angle : 0.662 10.619 19144 Z= 0.339 Chirality : 0.045 0.331 2138 Planarity : 0.005 0.053 2386 Dihedral : 8.021 110.994 1981 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 18.61 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.76 % Favored : 92.06 % Rotamer: Outliers : 0.13 % Allowed : 4.25 % Favored : 95.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.66 (0.21), residues: 1662 helix: 1.21 (0.22), residues: 579 sheet: -0.88 (0.30), residues: 310 loop : -1.55 (0.22), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 170 HIS 0.007 0.001 HIS C 201 PHE 0.037 0.002 PHE E 282 TYR 0.015 0.001 TYR B 301 ARG 0.005 0.000 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 374 time to evaluate : 1.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.9391 (mmm) cc_final: 0.8874 (mpp) REVERT: D 141 ASP cc_start: 0.8866 (t0) cc_final: 0.8506 (t0) REVERT: D 226 GLN cc_start: 0.9101 (tm-30) cc_final: 0.8861 (tm-30) REVERT: D 404 MET cc_start: 0.8480 (tmm) cc_final: 0.8158 (tmm) REVERT: D 408 ILE cc_start: 0.9204 (tp) cc_final: 0.8877 (tp) REVERT: D 412 PHE cc_start: 0.8531 (m-80) cc_final: 0.8271 (m-80) REVERT: A 159 PHE cc_start: 0.8842 (t80) cc_final: 0.8540 (t80) REVERT: A 220 MET cc_start: 0.8017 (pmm) cc_final: 0.7791 (pmm) REVERT: A 246 MET cc_start: 0.9431 (ppp) cc_final: 0.8773 (ppp) REVERT: A 274 LEU cc_start: 0.9497 (mp) cc_final: 0.9143 (tt) REVERT: A 287 MET cc_start: 0.9241 (mmm) cc_final: 0.8504 (mmm) REVERT: B 97 ASP cc_start: 0.8117 (p0) cc_final: 0.7654 (p0) REVERT: B 186 GLN cc_start: 0.8423 (pm20) cc_final: 0.7992 (pm20) REVERT: B 210 ILE cc_start: 0.9440 (pt) cc_final: 0.9196 (pt) REVERT: B 211 GLU cc_start: 0.7246 (pm20) cc_final: 0.6978 (pm20) REVERT: B 220 MET cc_start: 0.8508 (pmm) cc_final: 0.8275 (pmm) REVERT: B 239 TRP cc_start: 0.8334 (m-10) cc_final: 0.8053 (m-10) REVERT: B 242 PHE cc_start: 0.8112 (m-80) cc_final: 0.7790 (m-80) REVERT: C 17 LEU cc_start: 0.9266 (tp) cc_final: 0.8874 (tp) REVERT: C 18 MET cc_start: 0.8850 (pmm) cc_final: 0.8068 (pmm) REVERT: C 97 ASP cc_start: 0.7722 (p0) cc_final: 0.6974 (p0) REVERT: C 103 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7720 (tm-30) REVERT: C 404 MET cc_start: 0.8653 (ttt) cc_final: 0.8061 (tpp) REVERT: C 411 MET cc_start: 0.6525 (tpt) cc_final: 0.6062 (mmp) REVERT: E 77 MET cc_start: 0.7944 (tpp) cc_final: 0.7695 (tpp) REVERT: E 115 CYS cc_start: 0.8860 (t) cc_final: 0.8605 (t) REVERT: E 170 MET cc_start: 0.8311 (mmm) cc_final: 0.8065 (mmm) REVERT: E 173 GLN cc_start: 0.7754 (mm-40) cc_final: 0.7269 (mm110) REVERT: E 200 GLN cc_start: 0.8618 (mp10) cc_final: 0.8112 (mp10) REVERT: E 201 LEU cc_start: 0.6998 (tp) cc_final: 0.6759 (tp) REVERT: E 235 GLU cc_start: 0.7376 (tm-30) cc_final: 0.6602 (tm-30) REVERT: E 314 CYS cc_start: 0.9326 (m) cc_final: 0.9033 (m) REVERT: E 465 PHE cc_start: 0.8253 (p90) cc_final: 0.7063 (p90) outliers start: 2 outliers final: 0 residues processed: 375 average time/residue: 0.2179 time to fit residues: 124.0553 Evaluate side-chains 292 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 133 optimal weight: 8.9990 chunk 91 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 119 optimal weight: 8.9990 chunk 66 optimal weight: 0.9980 chunk 136 optimal weight: 8.9990 chunk 110 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 81 optimal weight: 0.8980 chunk 144 optimal weight: 10.0000 chunk 40 optimal weight: 0.0060 overall best weight: 2.3800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN A 61 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 138 ASN ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 14148 Z= 0.243 Angle : 0.654 10.432 19144 Z= 0.332 Chirality : 0.045 0.302 2138 Planarity : 0.004 0.048 2386 Dihedral : 7.715 110.182 1981 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 17.60 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.98 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -0.71 (0.21), residues: 1662 helix: 1.16 (0.22), residues: 585 sheet: -0.88 (0.30), residues: 309 loop : -1.61 (0.22), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 239 HIS 0.006 0.001 HIS C 201 PHE 0.033 0.002 PHE E 282 TYR 0.013 0.001 TYR B 301 ARG 0.004 0.000 ARG C 29 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 368 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.9406 (mmm) cc_final: 0.8872 (mpp) REVERT: D 145 PHE cc_start: 0.9248 (t80) cc_final: 0.9005 (t80) REVERT: D 226 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8834 (tm-30) REVERT: D 287 MET cc_start: 0.9113 (mmm) cc_final: 0.8657 (mmm) REVERT: D 404 MET cc_start: 0.8483 (tmm) cc_final: 0.8163 (tmm) REVERT: D 408 ILE cc_start: 0.9184 (tp) cc_final: 0.8843 (tp) REVERT: D 412 PHE cc_start: 0.8538 (m-80) cc_final: 0.8268 (m-80) REVERT: A 159 PHE cc_start: 0.8879 (t80) cc_final: 0.8598 (t80) REVERT: A 191 GLU cc_start: 0.7821 (tm-30) cc_final: 0.7543 (tm-30) REVERT: A 220 MET cc_start: 0.8077 (pmm) cc_final: 0.7773 (pmm) REVERT: A 274 LEU cc_start: 0.9494 (mp) cc_final: 0.9138 (tt) REVERT: A 287 MET cc_start: 0.9277 (mmm) cc_final: 0.8487 (mmm) REVERT: B 97 ASP cc_start: 0.8107 (p0) cc_final: 0.7655 (p0) REVERT: B 103 GLU cc_start: 0.7800 (pp20) cc_final: 0.7572 (pp20) REVERT: B 211 GLU cc_start: 0.7061 (pm20) cc_final: 0.6828 (pm20) REVERT: B 239 TRP cc_start: 0.8367 (m-10) cc_final: 0.8105 (m-10) REVERT: B 242 PHE cc_start: 0.8123 (m-80) cc_final: 0.7864 (m-80) REVERT: B 263 MET cc_start: 0.9324 (tpt) cc_final: 0.9111 (tpt) REVERT: C 17 LEU cc_start: 0.9263 (tp) cc_final: 0.8866 (tp) REVERT: C 18 MET cc_start: 0.8831 (pmm) cc_final: 0.8087 (pmm) REVERT: C 97 ASP cc_start: 0.7697 (p0) cc_final: 0.6948 (p0) REVERT: C 103 GLU cc_start: 0.8119 (tm-30) cc_final: 0.7688 (tm-30) REVERT: C 163 MET cc_start: 0.8646 (ptm) cc_final: 0.8410 (ptm) REVERT: C 167 ILE cc_start: 0.7836 (tt) cc_final: 0.7462 (tt) REVERT: C 404 MET cc_start: 0.8619 (ttt) cc_final: 0.8031 (tpp) REVERT: C 411 MET cc_start: 0.6498 (tpt) cc_final: 0.6001 (mmp) REVERT: E 77 MET cc_start: 0.7959 (tpp) cc_final: 0.7710 (tpp) REVERT: E 115 CYS cc_start: 0.8826 (t) cc_final: 0.8589 (t) REVERT: E 170 MET cc_start: 0.8324 (mmm) cc_final: 0.7951 (mmm) REVERT: E 173 GLN cc_start: 0.7816 (mm-40) cc_final: 0.7334 (mm110) REVERT: E 200 GLN cc_start: 0.8566 (mp10) cc_final: 0.8045 (mp10) REVERT: E 235 GLU cc_start: 0.7481 (tm-30) cc_final: 0.6675 (tm-30) REVERT: E 314 CYS cc_start: 0.9323 (m) cc_final: 0.9040 (m) REVERT: E 324 GLU cc_start: 0.8177 (pp20) cc_final: 0.7883 (mm-30) REVERT: E 465 PHE cc_start: 0.8331 (p90) cc_final: 0.7228 (p90) outliers start: 0 outliers final: 0 residues processed: 368 average time/residue: 0.2226 time to fit residues: 124.9958 Evaluate side-chains 292 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 53 optimal weight: 4.9990 chunk 144 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 94 optimal weight: 6.9990 chunk 39 optimal weight: 8.9990 chunk 160 optimal weight: 6.9990 chunk 133 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 13 optimal weight: 0.0060 chunk 84 optimal weight: 0.7980 chunk 154 optimal weight: 9.9990 overall best weight: 2.9602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 177 GLN A 61 ASN A 107 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 177 GLN ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14148 Z= 0.277 Angle : 0.667 10.041 19144 Z= 0.341 Chirality : 0.046 0.277 2138 Planarity : 0.004 0.043 2386 Dihedral : 7.752 110.022 1981 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.64 % Favored : 92.18 % Rotamer: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.71 (0.21), residues: 1662 helix: 1.19 (0.22), residues: 577 sheet: -0.93 (0.30), residues: 308 loop : -1.57 (0.22), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 89 HIS 0.006 0.001 HIS C 201 PHE 0.034 0.002 PHE E 282 TYR 0.015 0.001 TYR A 301 ARG 0.004 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 1.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.9406 (mmm) cc_final: 0.8903 (mpp) REVERT: D 226 GLN cc_start: 0.9102 (tm-30) cc_final: 0.8826 (tm-30) REVERT: D 242 PHE cc_start: 0.7151 (m-80) cc_final: 0.6950 (m-80) REVERT: D 287 MET cc_start: 0.9120 (mmm) cc_final: 0.8684 (mmm) REVERT: D 404 MET cc_start: 0.8488 (tmm) cc_final: 0.8156 (tmm) REVERT: D 408 ILE cc_start: 0.9170 (tp) cc_final: 0.8884 (tp) REVERT: D 412 PHE cc_start: 0.8532 (m-80) cc_final: 0.8142 (m-10) REVERT: A 107 HIS cc_start: 0.8753 (p90) cc_final: 0.7928 (p90) REVERT: A 159 PHE cc_start: 0.8895 (t80) cc_final: 0.8625 (t80) REVERT: A 220 MET cc_start: 0.8192 (pmm) cc_final: 0.7887 (pmm) REVERT: A 274 LEU cc_start: 0.9492 (mp) cc_final: 0.9139 (tt) REVERT: A 287 MET cc_start: 0.9238 (mmm) cc_final: 0.8476 (mmm) REVERT: A 404 MET cc_start: 0.8016 (tmm) cc_final: 0.7793 (tmm) REVERT: B 97 ASP cc_start: 0.8201 (p0) cc_final: 0.7735 (p0) REVERT: B 103 GLU cc_start: 0.7806 (pp20) cc_final: 0.7578 (pp20) REVERT: B 211 GLU cc_start: 0.7178 (pm20) cc_final: 0.6921 (pm20) REVERT: B 239 TRP cc_start: 0.8376 (m-10) cc_final: 0.8083 (m-10) REVERT: B 242 PHE cc_start: 0.8168 (m-80) cc_final: 0.7891 (m-80) REVERT: C 17 LEU cc_start: 0.9270 (tp) cc_final: 0.8891 (tp) REVERT: C 18 MET cc_start: 0.8849 (pmm) cc_final: 0.8125 (pmm) REVERT: C 97 ASP cc_start: 0.7755 (p0) cc_final: 0.7002 (p0) REVERT: C 98 LEU cc_start: 0.9050 (tp) cc_final: 0.8823 (tp) REVERT: C 102 ASN cc_start: 0.8247 (p0) cc_final: 0.7547 (p0) REVERT: C 163 MET cc_start: 0.8660 (ptm) cc_final: 0.8417 (ptm) REVERT: C 167 ILE cc_start: 0.7873 (tt) cc_final: 0.7508 (tt) REVERT: C 404 MET cc_start: 0.8706 (ttt) cc_final: 0.8069 (tpp) REVERT: C 406 PHE cc_start: 0.6109 (m-80) cc_final: 0.5906 (m-80) REVERT: C 411 MET cc_start: 0.6505 (tpt) cc_final: 0.5979 (mmp) REVERT: E 115 CYS cc_start: 0.8860 (t) cc_final: 0.8615 (t) REVERT: E 170 MET cc_start: 0.8304 (mmm) cc_final: 0.7933 (mmm) REVERT: E 173 GLN cc_start: 0.7937 (mm-40) cc_final: 0.7447 (mm110) REVERT: E 200 GLN cc_start: 0.8542 (mp10) cc_final: 0.8043 (mp10) REVERT: E 235 GLU cc_start: 0.7487 (tm-30) cc_final: 0.6769 (tm-30) REVERT: E 324 GLU cc_start: 0.8357 (pp20) cc_final: 0.7934 (mm-30) REVERT: E 465 PHE cc_start: 0.8322 (p90) cc_final: 0.7231 (p90) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.2155 time to fit residues: 118.7937 Evaluate side-chains 292 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 292 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 18 optimal weight: 0.5980 chunk 91 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 135 optimal weight: 7.9990 chunk 89 optimal weight: 0.7980 chunk 159 optimal weight: 2.9990 chunk 100 optimal weight: 8.9990 chunk 97 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 98 optimal weight: 0.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 155 GLN D 177 GLN A 61 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14148 Z= 0.192 Angle : 0.657 11.522 19144 Z= 0.329 Chirality : 0.046 0.276 2138 Planarity : 0.004 0.040 2386 Dihedral : 7.524 108.306 1981 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.60 % Favored : 94.22 % Rotamer: Outliers : 0.07 % Allowed : 1.26 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.65 (0.21), residues: 1662 helix: 1.26 (0.22), residues: 576 sheet: -0.92 (0.30), residues: 315 loop : -1.55 (0.22), residues: 771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 170 HIS 0.006 0.001 HIS C 201 PHE 0.042 0.002 PHE D 293 TYR 0.014 0.001 TYR A 301 ARG 0.004 0.000 ARG B 27 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 375 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 374 time to evaluate : 1.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.9410 (mmm) cc_final: 0.8897 (mpp) REVERT: D 145 PHE cc_start: 0.9074 (t80) cc_final: 0.8831 (t80) REVERT: D 226 GLN cc_start: 0.9074 (tm-30) cc_final: 0.8747 (tm-30) REVERT: D 287 MET cc_start: 0.9147 (mmm) cc_final: 0.8627 (mmm) REVERT: D 404 MET cc_start: 0.8474 (tmm) cc_final: 0.8125 (tmm) REVERT: D 408 ILE cc_start: 0.9154 (tp) cc_final: 0.8885 (tp) REVERT: D 412 PHE cc_start: 0.8534 (m-80) cc_final: 0.8229 (m-10) REVERT: A 56 MET cc_start: 0.8021 (ttt) cc_final: 0.7814 (tpt) REVERT: A 107 HIS cc_start: 0.8657 (p90) cc_final: 0.7870 (p90) REVERT: A 220 MET cc_start: 0.8139 (pmm) cc_final: 0.7772 (pmm) REVERT: A 274 LEU cc_start: 0.9493 (mp) cc_final: 0.9134 (tt) REVERT: A 287 MET cc_start: 0.9286 (mmm) cc_final: 0.8477 (mmm) REVERT: A 404 MET cc_start: 0.8046 (tmm) cc_final: 0.7827 (tmm) REVERT: B 97 ASP cc_start: 0.8093 (p0) cc_final: 0.7687 (p0) REVERT: B 102 ASN cc_start: 0.8161 (p0) cc_final: 0.7105 (p0) REVERT: B 186 GLN cc_start: 0.8279 (pm20) cc_final: 0.7840 (pm20) REVERT: B 263 MET cc_start: 0.9278 (tpt) cc_final: 0.9055 (tpt) REVERT: C 17 LEU cc_start: 0.9267 (tp) cc_final: 0.8881 (tp) REVERT: C 18 MET cc_start: 0.8825 (pmm) cc_final: 0.8129 (pmm) REVERT: C 97 ASP cc_start: 0.7673 (p0) cc_final: 0.6949 (p0) REVERT: C 98 LEU cc_start: 0.9023 (tp) cc_final: 0.8818 (tp) REVERT: C 102 ASN cc_start: 0.8239 (p0) cc_final: 0.7558 (p0) REVERT: C 103 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7614 (tm-30) REVERT: C 167 ILE cc_start: 0.7682 (tt) cc_final: 0.7295 (tt) REVERT: C 404 MET cc_start: 0.8633 (ttt) cc_final: 0.8045 (tpp) REVERT: C 411 MET cc_start: 0.6481 (tpt) cc_final: 0.5962 (mmp) REVERT: C 414 TRP cc_start: 0.8790 (m100) cc_final: 0.8498 (m100) REVERT: E 115 CYS cc_start: 0.8867 (t) cc_final: 0.8637 (t) REVERT: E 152 SER cc_start: 0.8482 (t) cc_final: 0.8263 (p) REVERT: E 170 MET cc_start: 0.8357 (mmm) cc_final: 0.7941 (mmm) REVERT: E 173 GLN cc_start: 0.7864 (mm-40) cc_final: 0.7321 (mm110) REVERT: E 200 GLN cc_start: 0.8557 (mp10) cc_final: 0.7943 (mp10) REVERT: E 314 CYS cc_start: 0.9261 (m) cc_final: 0.8944 (m) REVERT: E 324 GLU cc_start: 0.8350 (pp20) cc_final: 0.7893 (mm-30) REVERT: E 465 PHE cc_start: 0.8325 (p90) cc_final: 0.7222 (p90) outliers start: 1 outliers final: 0 residues processed: 374 average time/residue: 0.2178 time to fit residues: 124.2993 Evaluate side-chains 298 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 298 time to evaluate : 1.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 63 optimal weight: 5.9990 chunk 95 optimal weight: 1.9990 chunk 48 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 30 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 109 optimal weight: 0.2980 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 125 optimal weight: 0.5980 chunk 145 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN A 61 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 186 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14148 Z= 0.223 Angle : 0.659 9.338 19144 Z= 0.334 Chirality : 0.046 0.263 2138 Planarity : 0.004 0.038 2386 Dihedral : 7.469 108.096 1981 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.18 % Allowed : 7.16 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.62 (0.21), residues: 1662 helix: 1.36 (0.23), residues: 570 sheet: -0.96 (0.29), residues: 317 loop : -1.55 (0.22), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 239 HIS 0.005 0.001 HIS C 201 PHE 0.035 0.002 PHE B 242 TYR 0.014 0.001 TYR A 301 ARG 0.004 0.000 ARG C 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.9423 (mmm) cc_final: 0.8900 (mpp) REVERT: D 145 PHE cc_start: 0.9179 (t80) cc_final: 0.8921 (t80) REVERT: D 287 MET cc_start: 0.9169 (mmm) cc_final: 0.8638 (mmm) REVERT: D 404 MET cc_start: 0.8485 (tmm) cc_final: 0.8123 (tmm) REVERT: D 408 ILE cc_start: 0.9155 (tp) cc_final: 0.8861 (tp) REVERT: D 412 PHE cc_start: 0.8544 (m-80) cc_final: 0.8236 (m-10) REVERT: A 107 HIS cc_start: 0.8685 (p90) cc_final: 0.7861 (p90) REVERT: A 220 MET cc_start: 0.8245 (pmm) cc_final: 0.7890 (pmm) REVERT: A 274 LEU cc_start: 0.9492 (mp) cc_final: 0.9120 (tt) REVERT: A 287 MET cc_start: 0.9306 (mmm) cc_final: 0.8592 (mmm) REVERT: A 306 PHE cc_start: 0.8618 (t80) cc_final: 0.8230 (t80) REVERT: A 404 MET cc_start: 0.8082 (tmm) cc_final: 0.7867 (tmm) REVERT: B 97 ASP cc_start: 0.8113 (p0) cc_final: 0.7701 (p0) REVERT: B 102 ASN cc_start: 0.8145 (p0) cc_final: 0.7070 (p0) REVERT: B 110 GLU cc_start: 0.8178 (pt0) cc_final: 0.7933 (pt0) REVERT: B 173 GLN cc_start: 0.8996 (mp10) cc_final: 0.8571 (mp10) REVERT: C 17 LEU cc_start: 0.9263 (tp) cc_final: 0.8888 (tp) REVERT: C 18 MET cc_start: 0.8907 (pmm) cc_final: 0.8105 (pmm) REVERT: C 97 ASP cc_start: 0.7681 (p0) cc_final: 0.6954 (p0) REVERT: C 102 ASN cc_start: 0.8280 (p0) cc_final: 0.7529 (p0) REVERT: C 116 LYS cc_start: 0.8646 (mttm) cc_final: 0.8130 (mtmt) REVERT: C 163 MET cc_start: 0.8573 (ptm) cc_final: 0.8371 (ptm) REVERT: C 167 ILE cc_start: 0.7700 (tt) cc_final: 0.7300 (tt) REVERT: C 283 ILE cc_start: 0.8264 (tt) cc_final: 0.7880 (tt) REVERT: C 404 MET cc_start: 0.8666 (ttt) cc_final: 0.8065 (tpp) REVERT: C 406 PHE cc_start: 0.6058 (m-80) cc_final: 0.5623 (m-80) REVERT: C 411 MET cc_start: 0.6358 (tpt) cc_final: 0.5833 (mmp) REVERT: C 414 TRP cc_start: 0.8831 (m100) cc_final: 0.8517 (m100) REVERT: E 77 MET cc_start: 0.8111 (tpp) cc_final: 0.7849 (tpp) REVERT: E 115 CYS cc_start: 0.8868 (t) cc_final: 0.8631 (t) REVERT: E 152 SER cc_start: 0.8511 (t) cc_final: 0.8306 (p) REVERT: E 170 MET cc_start: 0.8365 (mmm) cc_final: 0.7965 (mmm) REVERT: E 173 GLN cc_start: 0.7979 (mm-40) cc_final: 0.7443 (mm110) REVERT: E 176 LYS cc_start: 0.9042 (ptmm) cc_final: 0.8091 (ptmt) REVERT: E 200 GLN cc_start: 0.8569 (mp10) cc_final: 0.7975 (mp10) REVERT: E 244 VAL cc_start: 0.8921 (t) cc_final: 0.8563 (t) REVERT: E 314 CYS cc_start: 0.9269 (m) cc_final: 0.8957 (m) REVERT: E 324 GLU cc_start: 0.8418 (pp20) cc_final: 0.7948 (mm-30) REVERT: E 465 PHE cc_start: 0.8365 (p90) cc_final: 0.7209 (p90) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.2200 time to fit residues: 122.0746 Evaluate side-chains 294 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 294 time to evaluate : 1.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 153 optimal weight: 0.9990 chunk 139 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 chunk 89 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 117 optimal weight: 0.0270 chunk 45 optimal weight: 9.9990 chunk 134 optimal weight: 0.0570 chunk 141 optimal weight: 5.9990 chunk 148 optimal weight: 1.9990 chunk 97 optimal weight: 9.9990 overall best weight: 0.8162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN A 61 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN A 186 GLN ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14148 Z= 0.186 Angle : 0.664 10.591 19144 Z= 0.332 Chirality : 0.046 0.273 2138 Planarity : 0.005 0.121 2386 Dihedral : 7.286 106.213 1981 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 15.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.54 % Favored : 94.28 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.64 (0.21), residues: 1662 helix: 1.30 (0.23), residues: 568 sheet: -0.87 (0.30), residues: 310 loop : -1.56 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 89 HIS 0.006 0.001 HIS C 201 PHE 0.030 0.002 PHE E 282 TYR 0.024 0.001 TYR B 301 ARG 0.009 0.000 ARG E 190 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 385 time to evaluate : 1.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 89 MET cc_start: 0.9423 (mmm) cc_final: 0.8895 (mpp) REVERT: D 145 PHE cc_start: 0.9110 (t80) cc_final: 0.8882 (t80) REVERT: D 287 MET cc_start: 0.9157 (mmm) cc_final: 0.8591 (mmm) REVERT: D 404 MET cc_start: 0.8478 (tmm) cc_final: 0.8131 (tmm) REVERT: D 408 ILE cc_start: 0.9152 (tp) cc_final: 0.8858 (tp) REVERT: D 412 PHE cc_start: 0.8523 (m-80) cc_final: 0.8234 (m-10) REVERT: A 107 HIS cc_start: 0.8583 (p90) cc_final: 0.7823 (p90) REVERT: A 159 PHE cc_start: 0.8737 (t80) cc_final: 0.8430 (t80) REVERT: A 220 MET cc_start: 0.8142 (pmm) cc_final: 0.7746 (pmm) REVERT: A 274 LEU cc_start: 0.9502 (mp) cc_final: 0.9113 (tt) REVERT: A 287 MET cc_start: 0.9309 (mmm) cc_final: 0.8636 (mmm) REVERT: A 404 MET cc_start: 0.8015 (tmm) cc_final: 0.7764 (tmm) REVERT: B 97 ASP cc_start: 0.8011 (p0) cc_final: 0.7534 (p0) REVERT: B 102 ASN cc_start: 0.8122 (p0) cc_final: 0.7089 (p0) REVERT: B 110 GLU cc_start: 0.8121 (pt0) cc_final: 0.7906 (pt0) REVERT: B 173 GLN cc_start: 0.8992 (mp10) cc_final: 0.8566 (mp10) REVERT: B 186 GLN cc_start: 0.8243 (pm20) cc_final: 0.7811 (pm20) REVERT: B 301 TYR cc_start: 0.8642 (t80) cc_final: 0.8292 (t80) REVERT: C 97 ASP cc_start: 0.7512 (p0) cc_final: 0.6787 (p0) REVERT: C 102 ASN cc_start: 0.8325 (p0) cc_final: 0.7540 (p0) REVERT: C 103 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7621 (tm-30) REVERT: C 116 LYS cc_start: 0.8692 (mttm) cc_final: 0.8134 (mtmt) REVERT: C 163 MET cc_start: 0.8551 (ptm) cc_final: 0.8331 (ptm) REVERT: C 167 ILE cc_start: 0.7577 (tt) cc_final: 0.7271 (tt) REVERT: C 168 PHE cc_start: 0.8299 (m-80) cc_final: 0.8056 (m-10) REVERT: C 404 MET cc_start: 0.8667 (ttt) cc_final: 0.8074 (tpp) REVERT: C 411 MET cc_start: 0.6350 (tpt) cc_final: 0.5805 (mmp) REVERT: C 414 TRP cc_start: 0.8773 (m100) cc_final: 0.8474 (m100) REVERT: E 77 MET cc_start: 0.8122 (tpp) cc_final: 0.7851 (tpp) REVERT: E 115 CYS cc_start: 0.8848 (t) cc_final: 0.8609 (t) REVERT: E 152 SER cc_start: 0.8475 (t) cc_final: 0.8262 (p) REVERT: E 170 MET cc_start: 0.8390 (mmm) cc_final: 0.7991 (mmm) REVERT: E 173 GLN cc_start: 0.7880 (mm-40) cc_final: 0.7287 (mm110) REVERT: E 190 ARG cc_start: 0.7956 (ppt170) cc_final: 0.7294 (tmm160) REVERT: E 244 VAL cc_start: 0.8703 (t) cc_final: 0.8501 (t) REVERT: E 314 CYS cc_start: 0.9244 (m) cc_final: 0.8925 (m) REVERT: E 324 GLU cc_start: 0.8346 (pp20) cc_final: 0.7912 (mm-30) outliers start: 0 outliers final: 0 residues processed: 385 average time/residue: 0.2201 time to fit residues: 129.5707 Evaluate side-chains 309 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 309 time to evaluate : 1.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 157 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 74 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 165 optimal weight: 8.9990 chunk 152 optimal weight: 0.2980 chunk 131 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 101 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 104 optimal weight: 0.3980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN A 61 ASN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 171 GLN ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 67 GLN ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 14148 Z= 0.186 Angle : 0.672 12.107 19144 Z= 0.332 Chirality : 0.046 0.294 2138 Planarity : 0.004 0.080 2386 Dihedral : 7.092 104.998 1981 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.90 % Favored : 93.92 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -0.68 (0.21), residues: 1662 helix: 1.23 (0.23), residues: 567 sheet: -0.77 (0.30), residues: 310 loop : -1.60 (0.21), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 89 HIS 0.005 0.001 HIS C 201 PHE 0.035 0.002 PHE E 282 TYR 0.022 0.001 TYR B 301 ARG 0.009 0.000 ARG E 190 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3324 Ramachandran restraints generated. 1662 Oldfield, 0 Emsley, 1662 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 387 time to evaluate : 1.668 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 140 MET cc_start: 0.7634 (mmm) cc_final: 0.7188 (mmm) REVERT: D 145 PHE cc_start: 0.9153 (t80) cc_final: 0.8924 (t80) REVERT: D 404 MET cc_start: 0.8447 (tmm) cc_final: 0.8108 (tmm) REVERT: D 408 ILE cc_start: 0.9154 (tp) cc_final: 0.8874 (tp) REVERT: D 412 PHE cc_start: 0.8465 (m-80) cc_final: 0.8196 (m-10) REVERT: A 107 HIS cc_start: 0.8498 (p90) cc_final: 0.7761 (p90) REVERT: A 220 MET cc_start: 0.8162 (pmm) cc_final: 0.7787 (pmm) REVERT: A 274 LEU cc_start: 0.9446 (mp) cc_final: 0.9092 (tt) REVERT: A 287 MET cc_start: 0.9303 (mmm) cc_final: 0.8636 (mmm) REVERT: A 404 MET cc_start: 0.8102 (tmm) cc_final: 0.7857 (tmm) REVERT: B 97 ASP cc_start: 0.8051 (p0) cc_final: 0.7581 (p0) REVERT: B 102 ASN cc_start: 0.8103 (p0) cc_final: 0.7095 (p0) REVERT: B 110 GLU cc_start: 0.8079 (pt0) cc_final: 0.7698 (pt0) REVERT: B 173 GLN cc_start: 0.9026 (mp10) cc_final: 0.8592 (mp10) REVERT: B 186 GLN cc_start: 0.8232 (pm20) cc_final: 0.7767 (pm20) REVERT: B 220 MET cc_start: 0.8419 (pmm) cc_final: 0.7912 (pmm) REVERT: B 301 TYR cc_start: 0.8577 (t80) cc_final: 0.8219 (t80) REVERT: C 97 ASP cc_start: 0.7460 (p0) cc_final: 0.6733 (p0) REVERT: C 102 ASN cc_start: 0.8279 (p0) cc_final: 0.7478 (p0) REVERT: C 103 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7623 (tm-30) REVERT: C 283 ILE cc_start: 0.8148 (tt) cc_final: 0.7605 (tt) REVERT: C 404 MET cc_start: 0.8689 (ttt) cc_final: 0.8022 (tpp) REVERT: C 411 MET cc_start: 0.6332 (tpt) cc_final: 0.5841 (mmp) REVERT: C 414 TRP cc_start: 0.8743 (m100) cc_final: 0.8477 (m100) REVERT: E 77 MET cc_start: 0.8091 (tpp) cc_final: 0.7836 (tpp) REVERT: E 115 CYS cc_start: 0.8860 (t) cc_final: 0.8619 (t) REVERT: E 152 SER cc_start: 0.8441 (t) cc_final: 0.8237 (p) REVERT: E 170 MET cc_start: 0.8384 (mmm) cc_final: 0.7996 (mmm) REVERT: E 173 GLN cc_start: 0.7866 (mm-40) cc_final: 0.7249 (mm110) REVERT: E 176 LYS cc_start: 0.8914 (ptmm) cc_final: 0.7989 (ptmt) REVERT: E 190 ARG cc_start: 0.7962 (ppt170) cc_final: 0.7328 (tmm160) REVERT: E 244 VAL cc_start: 0.8805 (t) cc_final: 0.8386 (t) REVERT: E 314 CYS cc_start: 0.9204 (m) cc_final: 0.8846 (m) REVERT: E 324 GLU cc_start: 0.8359 (pp20) cc_final: 0.7906 (mm-30) REVERT: E 329 GLN cc_start: 0.9038 (mm-40) cc_final: 0.8494 (mm-40) REVERT: E 465 PHE cc_start: 0.8450 (p90) cc_final: 0.7505 (p90) outliers start: 0 outliers final: 0 residues processed: 387 average time/residue: 0.2321 time to fit residues: 136.8172 Evaluate side-chains 310 residues out of total 1510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 310 time to evaluate : 1.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 166 random chunks: chunk 140 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 121 optimal weight: 7.9990 chunk 19 optimal weight: 0.3980 chunk 36 optimal weight: 0.5980 chunk 131 optimal weight: 0.0040 chunk 55 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN A 61 ASN ** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 GLN ** E 467 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.118493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.096701 restraints weight = 37032.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.099664 restraints weight = 20409.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.101656 restraints weight = 13559.550| |-----------------------------------------------------------------------------| r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 14148 Z= 0.205 Angle : 0.670 12.122 19144 Z= 0.332 Chirality : 0.045 0.262 2138 Planarity : 0.004 0.075 2386 Dihedral : 7.042 104.710 1981 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 16.12 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.62 % Favored : 93.20 % Rotamer: Outliers : 0.07 % Allowed : 0.33 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.67 (0.21), residues: 1662 helix: 1.23 (0.23), residues: 569 sheet: -0.80 (0.30), residues: 313 loop : -1.57 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 89 HIS 0.005 0.001 HIS C 201 PHE 0.040 0.002 PHE C 168 TYR 0.020 0.001 TYR B 301 ARG 0.009 0.000 ARG E 190 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3229.48 seconds wall clock time: 59 minutes 18.45 seconds (3558.45 seconds total)