Starting phenix.real_space_refine on Fri Feb 16 07:51:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn5_27555/02_2024/8dn5_27555_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn5_27555/02_2024/8dn5_27555.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn5_27555/02_2024/8dn5_27555.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn5_27555/02_2024/8dn5_27555.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn5_27555/02_2024/8dn5_27555_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dn5_27555/02_2024/8dn5_27555_trim_updated.pdb" } resolution = 3.63 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= 0.009 sd= 0.092 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 101 5.16 5 C 9271 2.51 5 N 2245 2.21 5 O 2464 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 465": "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: 14081 Number of models: 1 Model: "" Number of chains: 13 Chain: "D" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2768 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 15, 'TRANS': 324} Chain breaks: 1 Chain: "A" Number of atoms: 2778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2778 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 15, 'TRANS': 325} Chain breaks: 1 Chain: "B" Number of atoms: 2729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2729 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Chain: "C" Number of atoms: 2726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2726 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 320} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "E" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2685 Classifications: {'peptide': 331} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 16, 'TRANS': 314} Chain breaks: 1 Chain: "D" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "D" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 85 Unusual residues: {'DD9': 1, 'HEX': 5, 'HP6': 3, 'NAG': 1, 'UND': 1} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 97 Unusual residues: {'DD9': 2, 'HEX': 1, 'HP6': 1, 'NAG': 1, 'NBU': 2, 'UND': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} 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: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 78 Unusual residues: {'D10': 2, 'DD9': 1, 'HEX': 3, 'NAG': 1, 'NBU': 3} Inner-chain residues flagged as termini: ['pdbres="GLY B 503 "'] Classifications: {'peptide': 1, 'undetermined': 10} Modifications used: {'COO': 1} Link IDs: {None: 10} 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: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 48 Unusual residues: {'HEX': 2, 'HP6': 2, 'NAG': 1, 'NBU': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} 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: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 72 Unusual residues: {'D10': 1, 'HEX': 2, 'NAG': 1, 'NBU': 1, 'OCT': 2, 'UND': 1} Inner-chain residues flagged as termini: ['pdbres="GLY E 502 "'] Classifications: {'peptide': 1, 'undetermined': 8} Modifications used: {'COO': 1} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 7.86, per 1000 atoms: 0.56 Number of scatterers: 14081 At special positions: 0 Unit cell: (102.09, 127.82, 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 101 16.00 O 2464 8.00 N 2245 7.00 C 9271 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=2.03 Simple disulfide: pdb=" SG CYS E 161 " - pdb=" SG CYS E 175 " distance=2.03 Simple disulfide: pdb=" SG CYS E 221 " - pdb=" SG CYS E 233 " distance=2.05 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=2, symmetry=0 Links applied NAG-ASN " NAG A 502 " - " ASN A 38 " " NAG B 504 " - " ASN B 38 " " NAG C 502 " - " ASN C 38 " " NAG D 502 " - " ASN D 38 " " NAG E 503 " - " ASN E 220 " Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 5.59 Conformation dependent library (CDL) restraints added in 2.5 seconds 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3222 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 26 sheets defined 37.0% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.77 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 71 through 73 No H-bonds generated for 'chain 'D' and resid 71 through 73' Processing helix chain 'D' and resid 90 through 92 No H-bonds generated for 'chain 'D' and resid 90 through 92' 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 242 Proline residue: D 230 - end of helix Processing helix chain 'D' and resid 249 through 273 removed outlier: 3.991A pdb=" N SER D 273 " --> pdb=" O GLY D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 309 removed outlier: 3.642A pdb=" N TRP D 286 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 416 removed outlier: 3.647A pdb=" N ILE D 388 " --> pdb=" O ARG D 384 " (cutoff:3.500A) 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 90 through 92 No H-bonds generated for 'chain 'A' and resid 90 through 92' Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 221 through 242 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 249 through 273 removed outlier: 3.946A pdb=" N ARG A 271 " --> pdb=" O SER A 267 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ALA A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 5.049A pdb=" N SER A 273 " --> pdb=" O GLY A 269 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 309 Processing helix chain 'A' and resid 386 through 417 Proline residue: A 403 - end of helix Processing helix chain 'B' and resid 10 through 17 Processing helix chain 'B' and resid 20 through 22 No H-bonds generated for 'chain 'B' and resid 20 through 22' 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 90 through 92 No H-bonds generated for 'chain 'B' and resid 90 through 92' 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 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 221 through 242 Proline residue: B 230 - end of helix Processing helix chain 'B' and resid 249 through 271 removed outlier: 3.595A pdb=" N LEU B 255 " --> pdb=" O ALA B 251 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 307 removed outlier: 3.521A pdb=" N TRP B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 417 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 90 through 92 No H-bonds generated for 'chain 'C' and resid 90 through 92' Processing helix chain 'C' and resid 145 through 147 No H-bonds generated for 'chain 'C' and resid 145 through 147' Processing helix chain 'C' and resid 221 through 242 Proline residue: C 230 - end of helix Processing helix chain 'C' and resid 249 through 272 Processing helix chain 'C' and resid 282 through 309 removed outlier: 3.816A pdb=" N TRP C 286 " --> pdb=" O ALA C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 387 through 418 Proline residue: C 403 - end of helix Processing helix chain 'E' and resid 36 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 removed outlier: 4.146A pdb=" N TYR E 113 " --> pdb=" O PRO E 110 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LYS E 114 " --> pdb=" O THR E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 168 through 170 No H-bonds generated for 'chain 'E' and resid 168 through 170' Processing helix chain 'E' and resid 245 through 250 Processing helix chain 'E' and resid 252 through 268 Processing helix chain 'E' and resid 273 through 295 Proline residue: E 278 - end of helix 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 166 through 170 removed outlier: 5.891A pdb=" N VAL D 37 " --> pdb=" O ILE D 167 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N GLU D 169 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N VAL D 39 " --> pdb=" O GLU D 169 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 38 " --> pdb=" O ASN D 69 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ASN D 69 " --> pdb=" O ASN D 38 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER D 40 " --> pdb=" O GLN D 67 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TRP D 68 " --> pdb=" O VAL D 126 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N LEU D 118 " --> pdb=" O LEU D 85 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 57 through 61 Processing sheet with id= C, first strand: chain 'D' and resid 149 through 156 Processing sheet with id= D, first strand: chain 'D' and resid 195 through 197 removed outlier: 3.767A pdb=" N GLU D 211 " --> pdb=" O ARG D 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'D' and resid 200 through 202 removed outlier: 3.569A pdb=" N GLY D 205 " --> pdb=" O TYR D 202 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 168 through 170 removed outlier: 5.905A pdb=" N VAL A 39 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER A 40 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 65 " --> pdb=" O ASN A 42 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP A 68 " --> pdb=" O VAL A 126 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 43 through 45 Processing sheet with id= H, first strand: chain 'A' and resid 57 through 60 Processing sheet with id= I, first strand: chain 'A' and resid 98 through 100 Processing sheet with id= J, first strand: chain 'A' and resid 193 through 197 removed outlier: 3.794A pdb=" N GLU A 211 " --> pdb=" O ARG A 196 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'B' and resid 43 through 45 Processing sheet with id= L, first strand: chain 'B' and resid 57 through 60 Processing sheet with id= M, first strand: chain 'B' and resid 65 through 69 removed outlier: 3.709A pdb=" N TRP B 68 " --> pdb=" O VAL B 126 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 150 through 157 Processing sheet with id= O, first strand: chain 'B' and resid 194 through 197 removed outlier: 3.523A pdb=" N ASP B 194 " --> pdb=" O ARG B 213 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'B' and resid 200 through 202 Processing sheet with id= Q, first strand: chain 'C' and resid 37 through 41 removed outlier: 4.040A pdb=" N ILE C 167 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLU C 169 " --> pdb=" O VAL C 39 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'C' and resid 57 through 60 Processing sheet with id= S, first strand: chain 'C' and resid 65 through 69 removed outlier: 3.661A pdb=" N TRP C 68 " --> pdb=" O VAL C 126 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'C' and resid 149 through 157 Processing sheet with id= U, first strand: chain 'C' and resid 195 through 197 removed outlier: 3.548A pdb=" N GLU C 211 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'C' and resid 200 through 202 removed outlier: 3.693A pdb=" N GLY C 205 " --> pdb=" O TYR C 202 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'E' and resid 189 through 193 removed outlier: 6.480A pdb=" N VAL E 58 " --> pdb=" O ARG E 190 " (cutoff:3.500A) removed outlier: 7.517A pdb=" N ILE E 192 " --> pdb=" O VAL E 58 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL E 60 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASP E 59 " --> pdb=" O ASN E 90 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ASN E 90 " --> pdb=" O ASP E 59 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TRP E 89 " --> pdb=" O VAL E 149 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'E' and resid 176 through 180 Processing sheet with id= Y, first strand: chain 'E' and resid 223 through 225 removed outlier: 3.755A pdb=" N TYR E 225 " --> pdb=" O GLY E 229 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLY E 229 " --> pdb=" O TYR E 225 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'E' and resid 66 through 69 removed outlier: 7.101A pdb=" N ASN E 82 " --> pdb=" O ASN E 67 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1608 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: 3.59 Time building geometry restraints manager: 6.00 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: 3698 1.33 - 1.46: 4026 1.46 - 1.59: 6486 1.59 - 1.72: 0 1.72 - 1.85: 170 Bond restraints: 14380 Sorted by residual: bond pdb=" N THR D 208 " pdb=" CA THR D 208 " ideal model delta sigma weight residual 1.454 1.499 -0.044 1.27e-02 6.20e+03 1.22e+01 bond pdb=" N PHE D 207 " pdb=" CA PHE D 207 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.23e-02 6.61e+03 1.19e+01 bond pdb=" N GLY C 501 " pdb=" CA GLY C 501 " ideal model delta sigma weight residual 1.451 1.503 -0.052 1.60e-02 3.91e+03 1.06e+01 bond pdb=" N ALA B 272 " pdb=" CA ALA B 272 " ideal model delta sigma weight residual 1.462 1.502 -0.040 1.23e-02 6.61e+03 1.06e+01 bond pdb=" N GLY A 501 " pdb=" CA GLY A 501 " ideal model delta sigma weight residual 1.451 1.503 -0.052 1.60e-02 3.91e+03 1.05e+01 ... (remaining 14375 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.04: 377 106.04 - 113.03: 7433 113.03 - 120.02: 5146 120.02 - 127.00: 6226 127.00 - 133.99: 173 Bond angle restraints: 19355 Sorted by residual: angle pdb=" N MET B 246 " pdb=" CA MET B 246 " pdb=" C MET B 246 " ideal model delta sigma weight residual 111.28 102.08 9.20 1.09e+00 8.42e-01 7.12e+01 angle pdb=" N ILE B 244 " pdb=" CA ILE B 244 " pdb=" C ILE B 244 " ideal model delta sigma weight residual 108.44 99.53 8.91 1.55e+00 4.16e-01 3.31e+01 angle pdb=" N ALA B 272 " pdb=" CA ALA B 272 " pdb=" C ALA B 272 " ideal model delta sigma weight residual 110.70 118.86 -8.16 1.55e+00 4.16e-01 2.77e+01 angle pdb=" N CYS E 221 " pdb=" CA CYS E 221 " pdb=" C CYS E 221 " ideal model delta sigma weight residual 113.19 104.97 8.22 1.58e+00 4.01e-01 2.70e+01 angle pdb=" CA ILE B 244 " pdb=" C ILE B 244 " pdb=" O ILE B 244 " ideal model delta sigma weight residual 121.45 116.77 4.68 1.00e+00 1.00e+00 2.19e+01 ... (remaining 19350 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 8045 17.98 - 35.95: 508 35.95 - 53.93: 89 53.93 - 71.91: 17 71.91 - 89.89: 6 Dihedral angle restraints: 8665 sinusoidal: 3693 harmonic: 4972 Sorted by residual: dihedral pdb=" CB CYS C 138 " pdb=" SG CYS C 138 " pdb=" SG CYS C 152 " pdb=" CB CYS C 152 " ideal model delta sinusoidal sigma weight residual 93.00 49.85 43.15 1 1.00e+01 1.00e-02 2.60e+01 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 52.96 40.04 1 1.00e+01 1.00e-02 2.25e+01 dihedral pdb=" CB CYS A 138 " pdb=" SG CYS A 138 " pdb=" SG CYS A 152 " pdb=" CB CYS A 152 " ideal model delta sinusoidal sigma weight residual 93.00 54.48 38.52 1 1.00e+01 1.00e-02 2.09e+01 ... (remaining 8662 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 1997 0.095 - 0.190: 127 0.190 - 0.285: 13 0.285 - 0.380: 2 0.380 - 0.475: 2 Chirality restraints: 2141 Sorted by residual: chirality pdb=" C1 NAG A 502 " pdb=" ND2 ASN A 38 " pdb=" C2 NAG A 502 " pdb=" O5 NAG A 502 " both_signs ideal model delta sigma weight residual False -2.40 -1.93 -0.47 2.00e-01 2.50e+01 5.64e+00 chirality pdb=" C1 NAG E 503 " pdb=" ND2 ASN E 220 " pdb=" C2 NAG E 503 " pdb=" O5 NAG E 503 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.12e+00 chirality pdb=" CA ILE B 244 " pdb=" N ILE B 244 " pdb=" C ILE B 244 " pdb=" CB ILE B 244 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 2138 not shown) Planarity restraints: 2399 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 502 " -0.340 2.00e-02 2.50e+03 2.95e-01 1.09e+03 pdb=" C7 NAG A 502 " 0.079 2.00e-02 2.50e+03 pdb=" C8 NAG A 502 " -0.079 2.00e-02 2.50e+03 pdb=" N2 NAG A 502 " 0.523 2.00e-02 2.50e+03 pdb=" O7 NAG A 502 " -0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 504 " -0.337 2.00e-02 2.50e+03 2.91e-01 1.05e+03 pdb=" C7 NAG B 504 " 0.080 2.00e-02 2.50e+03 pdb=" C8 NAG B 504 " -0.151 2.00e-02 2.50e+03 pdb=" N2 NAG B 504 " 0.517 2.00e-02 2.50e+03 pdb=" O7 NAG B 504 " -0.109 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG C 502 " -0.329 2.00e-02 2.50e+03 2.86e-01 1.02e+03 pdb=" C7 NAG C 502 " 0.076 2.00e-02 2.50e+03 pdb=" C8 NAG C 502 " -0.055 2.00e-02 2.50e+03 pdb=" N2 NAG C 502 " 0.503 2.00e-02 2.50e+03 pdb=" O7 NAG C 502 " -0.195 2.00e-02 2.50e+03 ... (remaining 2396 not shown) Histogram of nonbonded interaction distances: 0.98 - 1.76: 3 1.76 - 2.55: 107 2.55 - 3.33: 17151 3.33 - 4.12: 32317 4.12 - 4.90: 59775 Warning: very small nonbonded interaction distances. Nonbonded interactions: 109353 Sorted by model distance: nonbonded pdb=" CE1 PHE C 159 " pdb=" N GLY C 501 " model vdw 0.981 3.420 nonbonded pdb=" CD2 LEU D 261 " pdb=" CE1 PHE E 282 " model vdw 1.194 3.760 nonbonded pdb=" CD1 PHE C 159 " pdb=" N GLY C 501 " model vdw 1.433 3.420 nonbonded pdb=" CD2 LEU D 261 " pdb=" CD1 PHE E 282 " model vdw 2.150 3.760 nonbonded pdb=" CE1 PHE A 159 " pdb=" N GLY A 501 " model vdw 2.163 3.420 ... (remaining 109348 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 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'B' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) selection = (chain 'C' and (resid 9 through 308 or resid 386 through 419)) selection = (chain 'D' and (resid 9 through 308 or resid 386 or (resid 387 and (name N or na \ me CA or name C or name O or name CB )) or resid 388 through 419)) } 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: 1.580 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: 6.660 Check model and map are aligned: 0.210 Set scattering table: 0.120 Process input model: 38.730 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.050 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 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 0.052 14380 Z= 0.265 Angle : 0.733 9.200 19355 Z= 0.419 Chirality : 0.051 0.475 2141 Planarity : 0.012 0.295 2394 Dihedral : 11.886 89.887 5413 Min Nonbonded Distance : 0.981 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.37 % Favored : 93.45 % Rotamer: Outliers : 1.52 % Allowed : 0.93 % Favored : 97.55 % 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: -0.87 (0.22), residues: 1664 helix: 2.47 (0.22), residues: 573 sheet: -2.68 (0.27), residues: 335 loop : -2.05 (0.21), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.001 TRP B 94 HIS 0.003 0.000 HIS D 201 PHE 0.023 0.001 PHE E 266 TYR 0.014 0.001 TYR D 301 ARG 0.003 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 284 time to evaluate : 1.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 411 MET cc_start: 0.7190 (tpp) cc_final: 0.6775 (mtt) REVERT: A 75 TYR cc_start: 0.8363 (p90) cc_final: 0.8153 (p90) REVERT: A 266 GLN cc_start: 0.7311 (mm110) cc_final: 0.7031 (mt0) REVERT: C 113 THR cc_start: 0.7933 (m) cc_final: 0.7713 (m) REVERT: E 133 ASP cc_start: 0.7650 (p0) cc_final: 0.7339 (p0) REVERT: E 152 SER cc_start: 0.8353 (p) cc_final: 0.7997 (p) outliers start: 23 outliers final: 8 residues processed: 303 average time/residue: 0.2311 time to fit residues: 106.0177 Evaluate side-chains 232 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 224 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 63 PHE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 270 SER Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain C residue 63 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 141 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 151 optimal weight: 0.0670 overall best weight: 0.9924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 125 ASN C 155 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8052 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14380 Z= 0.196 Angle : 0.643 9.362 19355 Z= 0.315 Chirality : 0.047 0.602 2141 Planarity : 0.004 0.032 2394 Dihedral : 7.227 87.902 2136 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.87 % Favored : 94.95 % Rotamer: Outliers : 2.85 % Allowed : 8.67 % Favored : 88.48 % 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: -0.66 (0.21), residues: 1664 helix: 2.65 (0.22), residues: 582 sheet: -2.37 (0.27), residues: 346 loop : -2.08 (0.21), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 94 HIS 0.003 0.000 HIS C 201 PHE 0.012 0.001 PHE A 409 TYR 0.011 0.001 TYR C 301 ARG 0.006 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 242 time to evaluate : 1.517 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 219 GLN cc_start: 0.8324 (mt0) cc_final: 0.8028 (mt0) REVERT: D 226 GLN cc_start: 0.6556 (mm-40) cc_final: 0.6167 (mm110) REVERT: E 133 ASP cc_start: 0.7782 (p0) cc_final: 0.7577 (p0) REVERT: E 152 SER cc_start: 0.8463 (p) cc_final: 0.8234 (p) outliers start: 43 outliers final: 33 residues processed: 268 average time/residue: 0.2268 time to fit residues: 93.2244 Evaluate side-chains 255 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 222 time to evaluate : 2.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 252 ARG Chi-restraints excluded: chain B residue 416 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 167 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 462 CYS Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 84 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 103 optimal weight: 0.5980 chunk 41 optimal weight: 10.0000 chunk 151 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 135 optimal weight: 10.0000 chunk 150 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 121 optimal weight: 6.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN E 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 14380 Z= 0.233 Angle : 0.602 8.598 19355 Z= 0.300 Chirality : 0.045 0.583 2141 Planarity : 0.004 0.036 2394 Dihedral : 6.519 78.073 2130 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.83 % Favored : 93.99 % Rotamer: Outliers : 3.18 % Allowed : 11.98 % Favored : 84.84 % 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: -0.56 (0.22), residues: 1664 helix: 2.80 (0.22), residues: 574 sheet: -2.26 (0.27), residues: 356 loop : -2.05 (0.21), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 267 HIS 0.002 0.001 HIS C 215 PHE 0.014 0.001 PHE A 44 TYR 0.016 0.001 TYR B 413 ARG 0.005 0.000 ARG D 399 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 231 time to evaluate : 1.725 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 219 GLN cc_start: 0.8391 (mt0) cc_final: 0.8163 (mt0) REVERT: B 226 GLN cc_start: 0.6830 (tm-30) cc_final: 0.6437 (tm-30) REVERT: B 287 MET cc_start: 0.6732 (OUTLIER) cc_final: 0.6339 (ttm) REVERT: E 152 SER cc_start: 0.8615 (p) cc_final: 0.8404 (p) REVERT: E 459 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7097 (t80) outliers start: 48 outliers final: 35 residues processed: 259 average time/residue: 0.2308 time to fit residues: 91.0723 Evaluate side-chains 257 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 220 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 67 GLN Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 98 SER Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 150 optimal weight: 0.1980 chunk 114 optimal weight: 0.4980 chunk 78 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 72 optimal weight: 7.9990 chunk 102 optimal weight: 10.0000 chunk 152 optimal weight: 4.9990 chunk 161 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 144 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14380 Z= 0.196 Angle : 0.581 8.346 19355 Z= 0.286 Chirality : 0.044 0.547 2141 Planarity : 0.003 0.029 2394 Dihedral : 6.197 71.326 2126 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.87 % Favored : 94.95 % Rotamer: Outliers : 3.51 % Allowed : 13.04 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.22), residues: 1664 helix: 2.92 (0.22), residues: 575 sheet: -2.14 (0.27), residues: 366 loop : -1.98 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.002 0.001 HIS D 107 PHE 0.014 0.001 PHE A 63 TYR 0.013 0.001 TYR B 413 ARG 0.005 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 230 time to evaluate : 1.490 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 219 GLN cc_start: 0.8378 (mt0) cc_final: 0.8160 (mt0) REVERT: A 89 MET cc_start: 0.8147 (ppp) cc_final: 0.7943 (ppp) REVERT: C 299 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8300 (mp) REVERT: E 152 SER cc_start: 0.8540 (p) cc_final: 0.8339 (p) outliers start: 53 outliers final: 41 residues processed: 261 average time/residue: 0.2161 time to fit residues: 87.2142 Evaluate side-chains 263 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 221 time to evaluate : 1.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 300 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 134 optimal weight: 0.0870 chunk 91 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 120 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 144 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 overall best weight: 2.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14380 Z= 0.330 Angle : 0.643 9.175 19355 Z= 0.321 Chirality : 0.045 0.542 2141 Planarity : 0.004 0.034 2394 Dihedral : 6.553 62.755 2126 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.91 % Favored : 92.97 % Rotamer: Outliers : 4.30 % Allowed : 14.49 % Favored : 81.20 % 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: -0.50 (0.22), residues: 1664 helix: 2.81 (0.21), residues: 573 sheet: -2.08 (0.28), residues: 352 loop : -2.07 (0.21), residues: 739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 267 HIS 0.003 0.001 HIS B 201 PHE 0.019 0.002 PHE B 293 TYR 0.018 0.002 TYR A 301 ARG 0.006 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 222 time to evaluate : 1.635 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: A 89 MET cc_start: 0.8235 (ppp) cc_final: 0.7938 (ppp) REVERT: A 283 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7693 (tt) REVERT: B 226 GLN cc_start: 0.6954 (tm-30) cc_final: 0.6596 (tm-30) REVERT: C 299 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8361 (mp) REVERT: E 276 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7645 (ttp80) REVERT: E 465 PHE cc_start: 0.8278 (t80) cc_final: 0.8014 (t80) outliers start: 65 outliers final: 44 residues processed: 261 average time/residue: 0.2299 time to fit residues: 92.0179 Evaluate side-chains 260 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 213 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 86 ASP Chi-restraints excluded: chain D residue 135 THR Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 208 THR Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 86 ASP Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 54 optimal weight: 1.9990 chunk 145 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 94 optimal weight: 0.0870 chunk 39 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 overall best weight: 1.0162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 115 ASN ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14380 Z= 0.169 Angle : 0.583 8.191 19355 Z= 0.287 Chirality : 0.043 0.520 2141 Planarity : 0.003 0.032 2394 Dihedral : 6.244 58.486 2126 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.05 % Favored : 94.77 % Rotamer: Outliers : 3.84 % Allowed : 16.41 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.22), residues: 1664 helix: 2.95 (0.22), residues: 574 sheet: -1.95 (0.28), residues: 347 loop : -1.96 (0.21), residues: 743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 414 HIS 0.002 0.001 HIS A 109 PHE 0.016 0.001 PHE A 63 TYR 0.013 0.001 TYR A 301 ARG 0.006 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 228 time to evaluate : 1.643 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: A 89 MET cc_start: 0.8233 (ppp) cc_final: 0.7961 (ppp) REVERT: A 415 ILE cc_start: 0.8696 (OUTLIER) cc_final: 0.8496 (tp) REVERT: B 226 GLN cc_start: 0.6685 (tm-30) cc_final: 0.6269 (tm-30) REVERT: B 227 MET cc_start: 0.7447 (mmm) cc_final: 0.6910 (mtt) REVERT: B 287 MET cc_start: 0.6766 (OUTLIER) cc_final: 0.6388 (ttm) REVERT: C 299 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8327 (mp) REVERT: C 407 LEU cc_start: 0.8679 (tt) cc_final: 0.8472 (tp) REVERT: E 276 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7574 (ttp80) REVERT: E 465 PHE cc_start: 0.8178 (t80) cc_final: 0.7959 (t80) outliers start: 58 outliers final: 41 residues processed: 258 average time/residue: 0.2286 time to fit residues: 90.5571 Evaluate side-chains 267 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 222 time to evaluate : 1.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 402 PHE Chi-restraints excluded: chain E residue 56 ILE Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 155 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 92 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 160 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14380 Z= 0.256 Angle : 0.605 8.494 19355 Z= 0.299 Chirality : 0.044 0.525 2141 Planarity : 0.003 0.034 2394 Dihedral : 6.419 60.013 2125 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.43 % Favored : 93.45 % Rotamer: Outliers : 3.97 % Allowed : 16.48 % Favored : 79.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.22), residues: 1664 helix: 2.88 (0.21), residues: 573 sheet: -1.95 (0.28), residues: 353 loop : -1.97 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 243 HIS 0.003 0.001 HIS B 201 PHE 0.017 0.001 PHE A 63 TYR 0.016 0.001 TYR D 301 ARG 0.006 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 217 time to evaluate : 1.652 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: A 89 MET cc_start: 0.8216 (ppp) cc_final: 0.7950 (ppp) REVERT: B 226 GLN cc_start: 0.6812 (tm-30) cc_final: 0.6398 (tm-30) REVERT: B 227 MET cc_start: 0.7439 (mmm) cc_final: 0.7010 (mtt) REVERT: C 299 LEU cc_start: 0.8695 (OUTLIER) cc_final: 0.8359 (mp) REVERT: E 276 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7650 (ttp80) REVERT: E 329 GLN cc_start: 0.8766 (tp40) cc_final: 0.8488 (tp40) outliers start: 60 outliers final: 43 residues processed: 252 average time/residue: 0.2273 time to fit residues: 88.0059 Evaluate side-chains 256 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 211 time to evaluate : 1.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 93 ILE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 96 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 31 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 109 optimal weight: 4.9990 chunk 79 optimal weight: 8.9990 chunk 15 optimal weight: 0.9980 chunk 126 optimal weight: 0.9980 chunk 146 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14380 Z= 0.197 Angle : 0.595 9.159 19355 Z= 0.293 Chirality : 0.043 0.513 2141 Planarity : 0.003 0.032 2394 Dihedral : 6.339 58.642 2125 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.41 % Favored : 94.41 % Rotamer: Outliers : 3.64 % Allowed : 17.74 % Favored : 78.62 % 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: -0.31 (0.22), residues: 1664 helix: 2.83 (0.22), residues: 579 sheet: -1.86 (0.28), residues: 347 loop : -1.94 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 414 HIS 0.002 0.001 HIS B 201 PHE 0.015 0.001 PHE A 63 TYR 0.014 0.001 TYR D 301 ARG 0.005 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 221 time to evaluate : 1.470 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 89 MET cc_start: 0.8249 (ppp) cc_final: 0.7984 (ppp) REVERT: B 226 GLN cc_start: 0.6764 (tm-30) cc_final: 0.6323 (tm-30) REVERT: B 227 MET cc_start: 0.7427 (mmm) cc_final: 0.6981 (mtt) REVERT: B 287 MET cc_start: 0.6801 (OUTLIER) cc_final: 0.6447 (ttm) REVERT: C 299 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8340 (mp) REVERT: E 276 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7608 (ttp80) REVERT: E 329 GLN cc_start: 0.8709 (tp40) cc_final: 0.8497 (tp40) outliers start: 55 outliers final: 46 residues processed: 252 average time/residue: 0.2322 time to fit residues: 89.0934 Evaluate side-chains 263 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 214 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 273 SER Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 292 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 154 optimal weight: 5.9990 chunk 140 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 90 optimal weight: 0.0670 chunk 65 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 135 optimal weight: 3.9990 chunk 141 optimal weight: 1.9990 chunk 98 optimal weight: 9.9990 chunk 158 optimal weight: 0.9980 overall best weight: 1.1722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14380 Z= 0.188 Angle : 0.598 9.975 19355 Z= 0.293 Chirality : 0.043 0.504 2141 Planarity : 0.003 0.031 2394 Dihedral : 6.215 55.590 2125 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.77 % Favored : 93.99 % Rotamer: Outliers : 3.51 % Allowed : 18.46 % Favored : 78.03 % 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 (0.22), residues: 1664 helix: 2.84 (0.22), residues: 579 sheet: -1.83 (0.28), residues: 348 loop : -1.92 (0.22), residues: 737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 414 HIS 0.001 0.000 HIS D 109 PHE 0.015 0.001 PHE A 63 TYR 0.014 0.001 TYR D 301 ARG 0.003 0.000 ARG A 271 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 1.732 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: A 89 MET cc_start: 0.8216 (ppp) cc_final: 0.7985 (ppp) REVERT: B 287 MET cc_start: 0.6830 (OUTLIER) cc_final: 0.6477 (ttm) REVERT: C 299 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8348 (mp) REVERT: E 276 ARG cc_start: 0.7853 (OUTLIER) cc_final: 0.7600 (ttp80) REVERT: E 329 GLN cc_start: 0.8700 (tp40) cc_final: 0.8454 (tp40) outliers start: 53 outliers final: 43 residues processed: 242 average time/residue: 0.2344 time to fit residues: 86.6777 Evaluate side-chains 257 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 211 time to evaluate : 1.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 96 optimal weight: 0.6980 chunk 75 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 166 optimal weight: 0.9980 chunk 153 optimal weight: 2.9990 chunk 132 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 chunk 102 optimal weight: 9.9990 chunk 81 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 141 optimal weight: 9.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14380 Z= 0.197 Angle : 0.602 10.625 19355 Z= 0.294 Chirality : 0.043 0.506 2141 Planarity : 0.003 0.032 2394 Dihedral : 6.153 54.676 2125 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.65 % Favored : 94.11 % Rotamer: Outliers : 3.24 % Allowed : 18.66 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1664 helix: 2.82 (0.22), residues: 579 sheet: -1.75 (0.29), residues: 337 loop : -1.91 (0.21), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 414 HIS 0.002 0.000 HIS D 109 PHE 0.016 0.001 PHE A 63 TYR 0.014 0.001 TYR D 301 ARG 0.005 0.000 ARG A 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3328 Ramachandran restraints generated. 1664 Oldfield, 0 Emsley, 1664 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 216 time to evaluate : 1.588 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: B 226 GLN cc_start: 0.6592 (tm-30) cc_final: 0.6309 (tm-30) REVERT: B 287 MET cc_start: 0.6846 (OUTLIER) cc_final: 0.6578 (ttm) REVERT: C 299 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8353 (mp) REVERT: E 276 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7583 (ttp80) REVERT: E 329 GLN cc_start: 0.8713 (tp40) cc_final: 0.8461 (tp40) outliers start: 49 outliers final: 45 residues processed: 240 average time/residue: 0.2243 time to fit residues: 82.3768 Evaluate side-chains 262 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 214 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 38 ASN Chi-restraints excluded: chain D residue 47 SER Chi-restraints excluded: chain D residue 211 GLU Chi-restraints excluded: chain D residue 412 PHE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 144 ASN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 280 VAL Chi-restraints excluded: chain A residue 287 MET Chi-restraints excluded: chain A residue 295 PHE Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 398 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 67 GLN Chi-restraints excluded: chain B residue 144 ASN Chi-restraints excluded: chain B residue 195 LEU Chi-restraints excluded: chain B residue 198 CYS Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 287 MET Chi-restraints excluded: chain B residue 293 PHE Chi-restraints excluded: chain B residue 411 MET Chi-restraints excluded: chain B residue 415 ILE Chi-restraints excluded: chain C residue 63 PHE Chi-restraints excluded: chain C residue 144 ASN Chi-restraints excluded: chain C residue 154 MET Chi-restraints excluded: chain C residue 253 VAL Chi-restraints excluded: chain C residue 260 VAL Chi-restraints excluded: chain C residue 283 ILE Chi-restraints excluded: chain C residue 285 ILE Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain E residue 36 ASN Chi-restraints excluded: chain E residue 72 ILE Chi-restraints excluded: chain E residue 109 ASP Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 120 ASP Chi-restraints excluded: chain E residue 152 SER Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 276 ARG Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 328 VAL Chi-restraints excluded: chain E residue 454 TYR Chi-restraints excluded: chain E residue 459 PHE Chi-restraints excluded: chain E residue 469 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 167 random chunks: chunk 40 optimal weight: 8.9990 chunk 122 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 36 optimal weight: 6.9990 chunk 132 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.139133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.113793 restraints weight = 20083.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116607 restraints weight = 12610.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.118446 restraints weight = 9287.205| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14380 Z= 0.204 Angle : 0.606 11.763 19355 Z= 0.295 Chirality : 0.043 0.502 2141 Planarity : 0.003 0.032 2394 Dihedral : 6.141 54.653 2125 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.01 % Favored : 93.75 % Rotamer: Outliers : 3.24 % Allowed : 18.66 % Favored : 78.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.22), residues: 1664 helix: 2.80 (0.22), residues: 580 sheet: -1.72 (0.29), residues: 337 loop : -1.91 (0.21), residues: 747 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 414 HIS 0.002 0.001 HIS B 201 PHE 0.016 0.001 PHE A 63 TYR 0.014 0.001 TYR C 128 ARG 0.005 0.000 ARG A 271 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2922.55 seconds wall clock time: 53 minutes 59.41 seconds (3239.41 seconds total)