Starting phenix.real_space_refine on Fri Aug 9 14:34:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u44_41874/08_2024/8u44_41874.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u44_41874/08_2024/8u44_41874.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u44_41874/08_2024/8u44_41874.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u44_41874/08_2024/8u44_41874.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u44_41874/08_2024/8u44_41874.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u44_41874/08_2024/8u44_41874.cif" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11763 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10683 2.51 5 N 2922 2.21 5 O 3342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 17028 Number of models: 1 Model: "" Number of chains: 15 Chain: "V" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 898 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "X" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "A" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2527 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "B" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1394 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "S" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 898 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "T" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "G" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2527 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "I" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1394 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "U" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 898 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "W" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 100} Chain: "H" Number of atoms: 2527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2527 Classifications: {'peptide': 322} Link IDs: {'PTRANS': 20, 'TRANS': 301} Chain: "J" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1394 Classifications: {'peptide': 173} Link IDs: {'PTRANS': 1, 'TRANS': 171} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "G" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 8.74, per 1000 atoms: 0.51 Number of scatterers: 17028 At special positions: 0 Unit cell: (130.625, 124.355, 146.3, 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 81 16.00 O 3342 8.00 N 2922 7.00 C 10683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=21, symmetry=0 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 94 " distance=2.04 Simple disulfide: pdb=" SG CYS X 23 " - pdb=" SG CYS X 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 277 " distance=2.03 Simple disulfide: pdb=" SG CYS A 64 " - pdb=" SG CYS A 76 " distance=2.03 Simple disulfide: pdb=" SG CYS A 97 " - pdb=" SG CYS A 139 " distance=2.03 Simple disulfide: pdb=" SG CYS A 281 " - pdb=" SG CYS A 305 " distance=2.06 Simple disulfide: pdb=" SG CYS B 144 " - pdb=" SG CYS B 148 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 94 " distance=2.04 Simple disulfide: pdb=" SG CYS T 23 " - pdb=" SG CYS T 88 " distance=2.03 Simple disulfide: pdb=" SG CYS G 52 " - pdb=" SG CYS G 277 " distance=2.03 Simple disulfide: pdb=" SG CYS G 64 " - pdb=" SG CYS G 76 " distance=2.03 Simple disulfide: pdb=" SG CYS G 97 " - pdb=" SG CYS G 139 " distance=2.03 Simple disulfide: pdb=" SG CYS G 281 " - pdb=" SG CYS G 305 " distance=2.06 Simple disulfide: pdb=" SG CYS I 144 " - pdb=" SG CYS I 148 " distance=2.03 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 94 " distance=2.04 Simple disulfide: pdb=" SG CYS W 23 " - pdb=" SG CYS W 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 52 " - pdb=" SG CYS H 277 " distance=2.03 Simple disulfide: pdb=" SG CYS H 64 " - pdb=" SG CYS H 76 " distance=2.03 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 139 " distance=2.03 Simple disulfide: pdb=" SG CYS H 281 " - pdb=" SG CYS H 305 " distance=2.06 Simple disulfide: pdb=" SG CYS J 144 " - pdb=" SG CYS J 148 " 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 21 " " NAG A 502 " - " ASN A 129 " " NAG A 503 " - " ASN A 289 " " NAG G 501 " - " ASN G 21 " " NAG G 502 " - " ASN G 129 " " NAG G 503 " - " ASN G 289 " " NAG H 501 " - " ASN H 21 " " NAG H 502 " - " ASN H 129 " " NAG H 503 " - " ASN H 289 " Time building additional restraints: 6.66 Conformation dependent library (CDL) restraints added in 2.9 seconds 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3954 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 42 sheets defined 18.8% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.03 Creating SS restraints... Processing helix chain 'V' and resid 85 through 89 Processing helix chain 'A' and resid 65 through 71 Processing helix chain 'A' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU A 77 " --> pdb=" O PRO A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 112 Processing helix chain 'A' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN A 191 " --> pdb=" O ASN A 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 58 Processing helix chain 'B' and resid 74 through 127 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET B 149 " --> pdb=" O ASN B 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) Processing helix chain 'S' and resid 85 through 89 Processing helix chain 'G' and resid 65 through 71 Processing helix chain 'G' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU G 77 " --> pdb=" O PRO G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 112 Processing helix chain 'G' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN G 191 " --> pdb=" O ASN G 187 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 58 Processing helix chain 'I' and resid 74 through 127 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET I 149 " --> pdb=" O ASN I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU I 165 " --> pdb=" O LYS I 161 " (cutoff:3.500A) Processing helix chain 'U' and resid 85 through 89 Processing helix chain 'H' and resid 65 through 71 Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.688A pdb=" N GLU H 77 " --> pdb=" O PRO H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 112 Processing helix chain 'H' and resid 187 through 195 removed outlier: 3.750A pdb=" N GLN H 191 " --> pdb=" O ASN H 187 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 58 Processing helix chain 'J' and resid 74 through 127 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 145 through 154 removed outlier: 4.226A pdb=" N MET J 149 " --> pdb=" O ASN J 145 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 170 removed outlier: 4.395A pdb=" N GLU J 164 " --> pdb=" O PRO J 160 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N GLU J 165 " --> pdb=" O LYS J 161 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'V' and resid 5 through 6 removed outlier: 4.203A pdb=" N ALA V 77 " --> pdb=" O CYS V 22 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N THR V 76 " --> pdb=" O ASP V 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP V 71 " --> pdb=" O THR V 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR V 69 " --> pdb=" O TYR V 78 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 10 through 12 removed outlier: 3.953A pdb=" N THR V 118 " --> pdb=" O GLU V 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS V 12 " --> pdb=" O THR V 118 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 47 through 49 Processing sheet with id=AA4, first strand: chain 'X' and resid 4 through 7 removed outlier: 4.545A pdb=" N VAL X 19 " --> pdb=" O ILE X 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE X 75 " --> pdb=" O VAL X 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE X 21 " --> pdb=" O LEU X 73 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS X 23 " --> pdb=" O PHE X 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE X 71 " --> pdb=" O CYS X 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP X 70 " --> pdb=" O SER X 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'X' and resid 53 through 54 removed outlier: 6.647A pdb=" N TRP X 35 " --> pdb=" O LEU X 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR X 85 " --> pdb=" O HIS X 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA7, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA8, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA9, first strand: chain 'A' and resid 100 through 102 removed outlier: 7.305A pdb=" N HIS A 101 " --> pdb=" O TYR A 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP A 234 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL A 178 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 151 through 152 Processing sheet with id=AB2, first strand: chain 'A' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP A 241 " --> pdb=" O ASN A 170 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 286 through 287 Processing sheet with id=AB4, first strand: chain 'A' and resid 294 through 295 removed outlier: 3.524A pdb=" N GLN A 295 " --> pdb=" O LYS A 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 130 through 132 Processing sheet with id=AB6, first strand: chain 'S' and resid 5 through 6 removed outlier: 4.202A pdb=" N ALA S 77 " --> pdb=" O CYS S 22 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR S 76 " --> pdb=" O ASP S 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP S 71 " --> pdb=" O THR S 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR S 69 " --> pdb=" O TYR S 78 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'S' and resid 10 through 12 removed outlier: 3.953A pdb=" N THR S 118 " --> pdb=" O GLU S 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS S 12 " --> pdb=" O THR S 118 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'S' and resid 47 through 49 Processing sheet with id=AB9, first strand: chain 'T' and resid 4 through 7 removed outlier: 4.546A pdb=" N VAL T 19 " --> pdb=" O ILE T 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE T 75 " --> pdb=" O VAL T 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE T 21 " --> pdb=" O LEU T 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS T 23 " --> pdb=" O PHE T 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE T 71 " --> pdb=" O CYS T 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP T 70 " --> pdb=" O SER T 67 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'T' and resid 53 through 54 removed outlier: 6.646A pdb=" N TRP T 35 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR T 85 " --> pdb=" O HIS T 38 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 25 through 26 Processing sheet with id=AC3, first strand: chain 'G' and resid 39 through 41 Processing sheet with id=AC4, first strand: chain 'G' and resid 88 through 89 Processing sheet with id=AC5, first strand: chain 'G' and resid 100 through 102 removed outlier: 7.306A pdb=" N HIS G 101 " --> pdb=" O TYR G 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP G 234 " --> pdb=" O HIS G 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 178 " --> pdb=" O THR G 235 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'G' and resid 151 through 152 Processing sheet with id=AC7, first strand: chain 'G' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP G 241 " --> pdb=" O ASN G 170 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 286 through 287 Processing sheet with id=AC9, first strand: chain 'G' and resid 294 through 295 removed outlier: 3.525A pdb=" N GLN G 295 " --> pdb=" O LYS G 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'I' and resid 130 through 132 Processing sheet with id=AD2, first strand: chain 'U' and resid 5 through 6 removed outlier: 4.202A pdb=" N ALA U 77 " --> pdb=" O CYS U 22 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR U 76 " --> pdb=" O ASP U 71 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASP U 71 " --> pdb=" O THR U 76 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N THR U 69 " --> pdb=" O TYR U 78 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'U' and resid 10 through 12 removed outlier: 3.952A pdb=" N THR U 118 " --> pdb=" O GLU U 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS U 12 " --> pdb=" O THR U 118 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'U' and resid 47 through 49 Processing sheet with id=AD5, first strand: chain 'W' and resid 4 through 7 removed outlier: 4.545A pdb=" N VAL W 19 " --> pdb=" O ILE W 75 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE W 75 " --> pdb=" O VAL W 19 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE W 21 " --> pdb=" O LEU W 73 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N CYS W 23 " --> pdb=" O PHE W 71 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE W 71 " --> pdb=" O CYS W 23 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ASP W 70 " --> pdb=" O SER W 67 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'W' and resid 53 through 54 removed outlier: 6.646A pdb=" N TRP W 35 " --> pdb=" O LEU W 47 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR W 85 " --> pdb=" O HIS W 38 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AD8, first strand: chain 'H' and resid 39 through 41 Processing sheet with id=AD9, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AE1, first strand: chain 'H' and resid 100 through 102 removed outlier: 7.305A pdb=" N HIS H 101 " --> pdb=" O TYR H 232 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N TRP H 234 " --> pdb=" O HIS H 101 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL H 178 " --> pdb=" O THR H 235 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 151 through 152 Processing sheet with id=AE3, first strand: chain 'H' and resid 167 through 170 removed outlier: 3.797A pdb=" N ASP H 241 " --> pdb=" O ASN H 170 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'H' and resid 286 through 287 Processing sheet with id=AE5, first strand: chain 'H' and resid 294 through 295 removed outlier: 3.525A pdb=" N GLN H 295 " --> pdb=" O LYS H 307 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'J' and resid 130 through 132 492 hydrogen bonds defined for protein. 1314 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: 4.63 Time building geometry restraints manager: 7.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 5580 1.35 - 1.47: 4354 1.47 - 1.59: 7364 1.59 - 1.72: 0 1.72 - 1.84: 114 Bond restraints: 17412 Sorted by residual: bond pdb=" N GLY B 1 " pdb=" CA GLY B 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" N GLY I 1 " pdb=" CA GLY I 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.03e+00 bond pdb=" N GLY J 1 " pdb=" CA GLY J 1 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.02e+00 bond pdb=" N GLU V 1 " pdb=" CA GLU V 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N GLU S 1 " pdb=" CA GLU S 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 ... (remaining 17407 not shown) Histogram of bond angle deviations from ideal: 99.20 - 106.16: 428 106.16 - 113.12: 8896 113.12 - 120.08: 6348 120.08 - 127.04: 7667 127.04 - 134.00: 247 Bond angle restraints: 23586 Sorted by residual: angle pdb=" CA TYR A 256 " pdb=" CB TYR A 256 " pdb=" CG TYR A 256 " ideal model delta sigma weight residual 113.90 121.94 -8.04 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CA TYR G 256 " pdb=" CB TYR G 256 " pdb=" CG TYR G 256 " ideal model delta sigma weight residual 113.90 121.94 -8.04 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CA TYR H 256 " pdb=" CB TYR H 256 " pdb=" CG TYR H 256 " ideal model delta sigma weight residual 113.90 121.93 -8.03 1.80e+00 3.09e-01 1.99e+01 angle pdb=" CB LEU J 99 " pdb=" CG LEU J 99 " pdb=" CD1 LEU J 99 " ideal model delta sigma weight residual 110.70 122.32 -11.62 3.00e+00 1.11e-01 1.50e+01 angle pdb=" CB LEU B 99 " pdb=" CG LEU B 99 " pdb=" CD1 LEU B 99 " ideal model delta sigma weight residual 110.70 122.32 -11.62 3.00e+00 1.11e-01 1.50e+01 ... (remaining 23581 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.96: 9288 16.96 - 33.91: 944 33.91 - 50.87: 175 50.87 - 67.82: 48 67.82 - 84.78: 36 Dihedral angle restraints: 10491 sinusoidal: 4284 harmonic: 6207 Sorted by residual: dihedral pdb=" CB CYS J 144 " pdb=" SG CYS J 144 " pdb=" SG CYS J 148 " pdb=" CB CYS J 148 " ideal model delta sinusoidal sigma weight residual -86.00 -159.24 73.24 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS B 144 " pdb=" SG CYS B 144 " pdb=" SG CYS B 148 " pdb=" CB CYS B 148 " ideal model delta sinusoidal sigma weight residual -86.00 -159.22 73.22 1 1.00e+01 1.00e-02 6.83e+01 dihedral pdb=" CB CYS I 144 " pdb=" SG CYS I 144 " pdb=" SG CYS I 148 " pdb=" CB CYS I 148 " ideal model delta sinusoidal sigma weight residual -86.00 -159.21 73.21 1 1.00e+01 1.00e-02 6.83e+01 ... (remaining 10488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1656 0.047 - 0.094: 625 0.094 - 0.141: 210 0.141 - 0.189: 62 0.189 - 0.236: 9 Chirality restraints: 2562 Sorted by residual: chirality pdb=" CA GLU J 103 " pdb=" N GLU J 103 " pdb=" C GLU J 103 " pdb=" CB GLU J 103 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLU I 103 " pdb=" N GLU I 103 " pdb=" C GLU I 103 " pdb=" CB GLU I 103 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA GLU B 103 " pdb=" N GLU B 103 " pdb=" C GLU B 103 " pdb=" CB GLU B 103 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.24 2.00e-01 2.50e+01 1.38e+00 ... (remaining 2559 not shown) Planarity restraints: 3066 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE H 124 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO H 125 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO H 125 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO H 125 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 124 " -0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO A 125 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 125 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 125 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE G 124 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.28e+00 pdb=" N PRO G 125 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO G 125 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 125 " 0.041 5.00e-02 4.00e+02 ... (remaining 3063 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 981 2.71 - 3.26: 17350 3.26 - 3.81: 27762 3.81 - 4.35: 35154 4.35 - 4.90: 59713 Nonbonded interactions: 140960 Sorted by model distance: nonbonded pdb=" NE2 GLN W 90 " pdb=" O PRO W 95 " model vdw 2.169 3.120 nonbonded pdb=" NE2 GLN X 90 " pdb=" O PRO X 95 " model vdw 2.169 3.120 nonbonded pdb=" NE2 GLN T 90 " pdb=" O PRO T 95 " model vdw 2.169 3.120 nonbonded pdb=" O SER H 22 " pdb=" ND2 ASN H 322 " model vdw 2.232 3.120 nonbonded pdb=" O SER A 22 " pdb=" ND2 ASN A 322 " model vdw 2.232 3.120 ... (remaining 140955 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'B' selection = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'S' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'T' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.180 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.400 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.080 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:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 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 : 0.006 0.056 17412 Z= 0.396 Angle : 1.009 11.622 23586 Z= 0.529 Chirality : 0.058 0.236 2562 Planarity : 0.006 0.076 3057 Dihedral : 14.786 84.781 6474 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.17), residues: 2145 helix: 0.11 (0.26), residues: 378 sheet: -2.20 (0.23), residues: 510 loop : -2.29 (0.16), residues: 1257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 69 HIS 0.005 0.001 HIS J 142 PHE 0.024 0.003 PHE B 70 TYR 0.027 0.002 TYR V 92 ARG 0.023 0.001 ARG V 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 355 time to evaluate : 1.749 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 113 GLN cc_start: 0.7953 (pt0) cc_final: 0.7612 (pm20) REVERT: X 55 GLN cc_start: 0.8407 (tp-100) cc_final: 0.8043 (tp-100) REVERT: X 100 GLN cc_start: 0.7988 (mm110) cc_final: 0.7343 (mp10) REVERT: B 17 MET cc_start: 0.6903 (mmm) cc_final: 0.6164 (tpp) REVERT: S 113 GLN cc_start: 0.8062 (pt0) cc_final: 0.7581 (pp30) REVERT: T 53 ASN cc_start: 0.8697 (m-40) cc_final: 0.8476 (m110) REVERT: T 55 GLN cc_start: 0.8438 (tp-100) cc_final: 0.8022 (tp-100) REVERT: T 100 GLN cc_start: 0.8130 (mm110) cc_final: 0.7607 (mp10) REVERT: I 42 GLN cc_start: 0.7949 (tp-100) cc_final: 0.7723 (tp40) REVERT: U 113 GLN cc_start: 0.8025 (pt0) cc_final: 0.7667 (pm20) REVERT: W 100 GLN cc_start: 0.7911 (mm110) cc_final: 0.7330 (mp10) REVERT: J 17 MET cc_start: 0.6739 (mmm) cc_final: 0.6306 (tpp) outliers start: 0 outliers final: 0 residues processed: 355 average time/residue: 0.2910 time to fit residues: 153.3218 Evaluate side-chains 199 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 199 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 89 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 108 optimal weight: 0.1980 chunk 86 optimal weight: 8.9990 chunk 166 optimal weight: 3.9990 chunk 64 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 124 optimal weight: 4.9990 chunk 193 optimal weight: 6.9990 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 ASN ** B 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 50 ASN B 114 ASN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN G 199 ASN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 114 ASN ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 114 ASN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.3013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17412 Z= 0.338 Angle : 0.684 10.673 23586 Z= 0.361 Chirality : 0.050 0.217 2562 Planarity : 0.005 0.050 3057 Dihedral : 5.685 55.145 2523 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 1.62 % Allowed : 10.79 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.18), residues: 2145 helix: 0.43 (0.27), residues: 366 sheet: -2.37 (0.23), residues: 483 loop : -2.18 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP U 45 HIS 0.005 0.001 HIS X 38 PHE 0.025 0.002 PHE U 53 TYR 0.016 0.002 TYR W 86 ARG 0.008 0.001 ARG G 220 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 217 time to evaluate : 2.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 78 TYR cc_start: 0.7137 (m-80) cc_final: 0.6925 (m-80) REVERT: V 85 ARG cc_start: 0.7035 (mtm110) cc_final: 0.6827 (mtm110) REVERT: B 17 MET cc_start: 0.6967 (mmm) cc_final: 0.6655 (tpp) REVERT: B 27 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7315 (tm-30) REVERT: S 13 LYS cc_start: 0.7683 (tptt) cc_final: 0.7471 (tptt) REVERT: I 27 GLN cc_start: 0.7518 (tm-30) cc_final: 0.7310 (tm-30) REVERT: U 13 LYS cc_start: 0.7874 (tptt) cc_final: 0.7534 (tptt) REVERT: U 85 ARG cc_start: 0.7283 (mtm110) cc_final: 0.6899 (ptp-170) REVERT: J 27 GLN cc_start: 0.7594 (tm-30) cc_final: 0.7394 (tm-30) outliers start: 30 outliers final: 14 residues processed: 242 average time/residue: 0.2914 time to fit residues: 108.3373 Evaluate side-chains 189 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 175 time to evaluate : 1.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 116 MET Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain H residue 158 ASN Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain J residue 40 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 160 optimal weight: 8.9990 chunk 131 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 193 optimal weight: 5.9990 chunk 209 optimal weight: 1.9990 chunk 172 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 66 optimal weight: 8.9990 chunk 155 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 6 GLN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 GLN G 183 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN H 199 ASN ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 50 ASN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 17412 Z= 0.373 Angle : 0.684 8.745 23586 Z= 0.358 Chirality : 0.049 0.195 2562 Planarity : 0.005 0.044 3057 Dihedral : 5.638 44.341 2523 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 1.78 % Allowed : 16.45 % Favored : 81.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.36 (0.17), residues: 2145 helix: 0.45 (0.27), residues: 366 sheet: -1.94 (0.27), residues: 393 loop : -2.13 (0.16), residues: 1386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 153 HIS 0.005 0.001 HIS H 184 PHE 0.016 0.002 PHE A 258 TYR 0.013 0.002 TYR U 92 ARG 0.004 0.001 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 204 time to evaluate : 2.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 108 MET cc_start: 0.7299 (tpp) cc_final: 0.6614 (tpp) REVERT: B 17 MET cc_start: 0.6887 (mmm) cc_final: 0.6570 (tpp) REVERT: B 27 GLN cc_start: 0.7899 (tm-30) cc_final: 0.7272 (tm-30) REVERT: B 98 LEU cc_start: 0.9111 (mm) cc_final: 0.8804 (mm) REVERT: S 53 PHE cc_start: 0.7002 (OUTLIER) cc_final: 0.5664 (m-80) REVERT: G 268 ILE cc_start: 0.6886 (OUTLIER) cc_final: 0.6553 (tt) REVERT: U 53 PHE cc_start: 0.6954 (OUTLIER) cc_final: 0.5341 (m-80) REVERT: W 32 TYR cc_start: 0.7818 (m-80) cc_final: 0.7575 (m-80) REVERT: H 258 PHE cc_start: 0.7988 (m-10) cc_final: 0.7655 (m-10) REVERT: J 17 MET cc_start: 0.6989 (tpp) cc_final: 0.6787 (mpp) REVERT: J 27 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7135 (tm-30) outliers start: 33 outliers final: 16 residues processed: 231 average time/residue: 0.2522 time to fit residues: 91.2272 Evaluate side-chains 193 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 174 time to evaluate : 1.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain A residue 125 SER Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 204 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain H residue 260 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 20.0000 chunk 145 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 92 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 194 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 184 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 overall best weight: 1.0082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 34 ASN T 55 GLN G 111 GLN I 125 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7549 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 17412 Z= 0.185 Angle : 0.585 8.455 23586 Z= 0.306 Chirality : 0.046 0.170 2562 Planarity : 0.004 0.048 3057 Dihedral : 4.847 32.084 2523 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.40 % Allowed : 19.09 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.94 (0.18), residues: 2145 helix: 0.65 (0.27), residues: 384 sheet: -1.44 (0.29), residues: 357 loop : -1.92 (0.16), residues: 1404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 111 HIS 0.005 0.001 HIS I 142 PHE 0.015 0.001 PHE T 49 TYR 0.012 0.001 TYR H 17 ARG 0.003 0.000 ARG S 96 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 228 time to evaluate : 1.828 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 53 PHE cc_start: 0.6800 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: B 17 MET cc_start: 0.6954 (mmm) cc_final: 0.6695 (tpp) REVERT: B 27 GLN cc_start: 0.7735 (tm-30) cc_final: 0.7442 (tm-30) REVERT: B 98 LEU cc_start: 0.9100 (mm) cc_final: 0.8853 (mm) REVERT: G 268 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6364 (tt) REVERT: I 27 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7212 (tm-30) REVERT: W 55 GLN cc_start: 0.8913 (tp40) cc_final: 0.8510 (tp-100) REVERT: J 27 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7108 (tm-30) outliers start: 26 outliers final: 18 residues processed: 251 average time/residue: 0.2544 time to fit residues: 100.8737 Evaluate side-chains 207 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 187 time to evaluate : 1.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 62 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 62 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 126 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 153 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 175 optimal weight: 0.9990 chunk 142 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 105 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 chunk 51 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN G 111 GLN I 169 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 183 HIS ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.4298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 17412 Z= 0.412 Angle : 0.714 9.689 23586 Z= 0.371 Chirality : 0.048 0.192 2562 Planarity : 0.005 0.043 3057 Dihedral : 5.159 35.320 2523 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.83 % Favored : 92.17 % Rotamer: Outliers : 3.07 % Allowed : 19.85 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.18), residues: 2145 helix: 0.58 (0.27), residues: 366 sheet: -1.48 (0.26), residues: 462 loop : -1.82 (0.16), residues: 1317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP V 111 HIS 0.005 0.002 HIS G 184 PHE 0.032 0.002 PHE H 121 TYR 0.014 0.002 TYR S 92 ARG 0.004 0.001 ARG A 120 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 182 time to evaluate : 1.835 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 53 PHE cc_start: 0.7222 (OUTLIER) cc_final: 0.6156 (m-80) REVERT: V 108 MET cc_start: 0.7252 (tpp) cc_final: 0.6837 (tpp) REVERT: B 27 GLN cc_start: 0.7890 (tm-30) cc_final: 0.7575 (tm-30) REVERT: B 98 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8875 (mm) REVERT: S 53 PHE cc_start: 0.7038 (OUTLIER) cc_final: 0.5630 (m-80) REVERT: G 268 ILE cc_start: 0.6854 (OUTLIER) cc_final: 0.6536 (tt) REVERT: I 27 GLN cc_start: 0.7780 (tm-30) cc_final: 0.7218 (tm-30) REVERT: I 42 GLN cc_start: 0.8960 (OUTLIER) cc_final: 0.8692 (mm-40) REVERT: U 53 PHE cc_start: 0.6939 (OUTLIER) cc_final: 0.5370 (m-80) REVERT: U 108 MET cc_start: 0.7037 (tpp) cc_final: 0.6482 (tpp) REVERT: J 27 GLN cc_start: 0.7658 (tm-30) cc_final: 0.7095 (tm-30) outliers start: 57 outliers final: 36 residues processed: 226 average time/residue: 0.2405 time to fit residues: 87.4495 Evaluate side-chains 207 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 165 time to evaluate : 1.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain V residue 116 MET Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 40 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain G residue 268 ILE Chi-restraints excluded: chain I residue 42 GLN Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain U residue 89 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 0.5980 chunk 185 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 120 optimal weight: 9.9990 chunk 50 optimal weight: 1.9990 chunk 206 optimal weight: 4.9990 chunk 171 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 17 optimal weight: 10.0000 chunk 68 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 overall best weight: 1.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: V 57 ASN ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN T 55 GLN G 111 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 95 ASN H 111 GLN ** J 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 17412 Z= 0.190 Angle : 0.607 8.437 23586 Z= 0.313 Chirality : 0.045 0.168 2562 Planarity : 0.004 0.050 3057 Dihedral : 4.668 31.130 2523 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 1.94 % Allowed : 21.04 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 2145 helix: 0.57 (0.27), residues: 384 sheet: -1.55 (0.28), residues: 417 loop : -1.75 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 111 HIS 0.004 0.001 HIS H 130 PHE 0.024 0.001 PHE H 121 TYR 0.013 0.001 TYR G 17 ARG 0.003 0.000 ARG S 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 220 time to evaluate : 1.926 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: symmetry clash revert: symmetry clash REVERT: V 53 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6048 (m-80) REVERT: V 108 MET cc_start: 0.7393 (tpp) cc_final: 0.6933 (tpp) REVERT: B 17 MET cc_start: 0.6828 (mmm) cc_final: 0.6387 (tpp) REVERT: B 98 LEU cc_start: 0.9136 (mm) cc_final: 0.8804 (mm) REVERT: S 57 ASN cc_start: 0.7387 (OUTLIER) cc_final: 0.7152 (t0) REVERT: I 6 ILE cc_start: 0.8499 (tt) cc_final: 0.8281 (pt) REVERT: I 27 GLN cc_start: 0.7728 (tm-30) cc_final: 0.7168 (tm-30) REVERT: U 72 ASP cc_start: 0.8156 (m-30) cc_final: 0.7951 (m-30) REVERT: U 108 MET cc_start: 0.7089 (tpp) cc_final: 0.6371 (tpp) REVERT: J 27 GLN cc_start: 0.7627 (tm-30) cc_final: 0.7016 (tm-30) REVERT: J 98 LEU cc_start: 0.8995 (mm) cc_final: 0.8729 (mm) outliers start: 36 outliers final: 24 residues processed: 251 average time/residue: 0.2702 time to fit residues: 107.0064 Evaluate side-chains 212 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 186 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 90 GLN Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 173 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 205 optimal weight: 7.9990 chunk 128 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 94 optimal weight: 0.5980 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN A 183 HIS ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN G 111 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN H 111 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 17412 Z= 0.314 Angle : 0.669 8.711 23586 Z= 0.345 Chirality : 0.047 0.329 2562 Planarity : 0.004 0.044 3057 Dihedral : 4.877 32.194 2523 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 2.27 % Allowed : 20.98 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.18), residues: 2145 helix: 0.49 (0.27), residues: 384 sheet: -1.53 (0.28), residues: 420 loop : -1.77 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 111 HIS 0.004 0.001 HIS H 184 PHE 0.019 0.002 PHE H 121 TYR 0.024 0.002 TYR S 58 ARG 0.003 0.000 ARG A 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 187 time to evaluate : 2.095 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: V 53 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6108 (m-80) REVERT: V 108 MET cc_start: 0.7301 (tpp) cc_final: 0.6876 (tpp) REVERT: B 17 MET cc_start: 0.6974 (mmm) cc_final: 0.6218 (tpp) REVERT: B 98 LEU cc_start: 0.9146 (mm) cc_final: 0.8886 (mm) REVERT: T 55 GLN cc_start: 0.9050 (tp40) cc_final: 0.8708 (tp-100) REVERT: I 27 GLN cc_start: 0.7815 (tm-30) cc_final: 0.7247 (tm-30) REVERT: I 42 GLN cc_start: 0.8820 (tp40) cc_final: 0.8249 (tp-100) REVERT: I 98 LEU cc_start: 0.8999 (mm) cc_final: 0.8734 (mm) REVERT: U 108 MET cc_start: 0.7077 (tpp) cc_final: 0.6480 (tpp) REVERT: W 55 GLN cc_start: 0.8784 (tp-100) cc_final: 0.8555 (tp-100) REVERT: J 27 GLN cc_start: 0.7654 (tm-30) cc_final: 0.7022 (tm-30) REVERT: J 98 LEU cc_start: 0.9060 (mm) cc_final: 0.8774 (mm) outliers start: 42 outliers final: 33 residues processed: 226 average time/residue: 0.2465 time to fit residues: 89.1002 Evaluate side-chains 209 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 175 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 6.9990 chunk 81 optimal weight: 0.9980 chunk 122 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 130 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 161 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN G 111 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 169 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17412 Z= 0.239 Angle : 0.641 11.586 23586 Z= 0.327 Chirality : 0.047 0.275 2562 Planarity : 0.004 0.053 3057 Dihedral : 4.717 30.274 2523 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.37 % Allowed : 21.41 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.18), residues: 2145 helix: 0.55 (0.27), residues: 384 sheet: -1.53 (0.28), residues: 420 loop : -1.75 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP V 111 HIS 0.004 0.001 HIS I 142 PHE 0.017 0.001 PHE H 121 TYR 0.015 0.001 TYR S 58 ARG 0.003 0.000 ARG H 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 193 time to evaluate : 1.854 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: V 53 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6087 (m-80) REVERT: V 108 MET cc_start: 0.7303 (tpp) cc_final: 0.6865 (tpp) REVERT: B 17 MET cc_start: 0.6996 (mmm) cc_final: 0.6261 (tpp) REVERT: B 98 LEU cc_start: 0.9156 (OUTLIER) cc_final: 0.8907 (mm) REVERT: S 53 PHE cc_start: 0.6934 (OUTLIER) cc_final: 0.5820 (m-80) REVERT: T 55 GLN cc_start: 0.9033 (tp40) cc_final: 0.8743 (tp-100) REVERT: I 27 GLN cc_start: 0.7757 (tm-30) cc_final: 0.7184 (tm-30) REVERT: I 98 LEU cc_start: 0.8988 (mm) cc_final: 0.8714 (mm) REVERT: U 108 MET cc_start: 0.7151 (tpp) cc_final: 0.6542 (tpp) REVERT: U 116 MET cc_start: 0.6559 (mmm) cc_final: 0.6345 (mmm) REVERT: W 55 GLN cc_start: 0.8815 (tp-100) cc_final: 0.8569 (tp-100) REVERT: J 27 GLN cc_start: 0.7680 (tm-30) cc_final: 0.7061 (tm-30) REVERT: J 42 GLN cc_start: 0.8269 (OUTLIER) cc_final: 0.7825 (tp-100) REVERT: J 98 LEU cc_start: 0.9055 (mm) cc_final: 0.8770 (mm) outliers start: 44 outliers final: 31 residues processed: 228 average time/residue: 0.2408 time to fit residues: 87.7096 Evaluate side-chains 218 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 183 time to evaluate : 1.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 42 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 0.8980 chunk 196 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 83 optimal weight: 5.9990 chunk 150 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 172 optimal weight: 7.9990 chunk 180 optimal weight: 9.9990 chunk 190 optimal weight: 5.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN G 111 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 17412 Z= 0.380 Angle : 0.725 12.323 23586 Z= 0.372 Chirality : 0.048 0.236 2562 Planarity : 0.005 0.055 3057 Dihedral : 5.150 32.858 2523 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 17.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 2.59 % Allowed : 21.47 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.18), residues: 2145 helix: 0.34 (0.27), residues: 384 sheet: -1.26 (0.27), residues: 432 loop : -1.77 (0.16), residues: 1329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP V 45 HIS 0.007 0.001 HIS H 184 PHE 0.015 0.002 PHE J 140 TYR 0.022 0.002 TYR V 58 ARG 0.006 0.000 ARG G 120 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 178 time to evaluate : 2.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 53 PHE cc_start: 0.7375 (OUTLIER) cc_final: 0.6157 (m-80) REVERT: V 108 MET cc_start: 0.7213 (tpp) cc_final: 0.6778 (tpp) REVERT: B 17 MET cc_start: 0.6974 (mmm) cc_final: 0.6670 (tpp) REVERT: B 98 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8938 (mm) REVERT: S 53 PHE cc_start: 0.7127 (OUTLIER) cc_final: 0.5731 (m-80) REVERT: I 27 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7278 (tm-30) REVERT: I 98 LEU cc_start: 0.9041 (mm) cc_final: 0.8757 (mm) REVERT: U 53 PHE cc_start: 0.7091 (OUTLIER) cc_final: 0.5339 (m-80) REVERT: U 93 TYR cc_start: 0.7664 (m-80) cc_final: 0.7448 (m-80) REVERT: U 108 MET cc_start: 0.7073 (tpp) cc_final: 0.6485 (tpp) REVERT: U 116 MET cc_start: 0.6504 (mmm) cc_final: 0.6033 (mmm) REVERT: H 258 PHE cc_start: 0.8079 (m-10) cc_final: 0.7659 (m-10) REVERT: J 27 GLN cc_start: 0.7722 (tm-30) cc_final: 0.7077 (tm-30) REVERT: J 42 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7989 (tp-100) REVERT: J 98 LEU cc_start: 0.9112 (mm) cc_final: 0.8794 (mm) outliers start: 48 outliers final: 39 residues processed: 219 average time/residue: 0.2446 time to fit residues: 85.9013 Evaluate side-chains 214 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 170 time to evaluate : 2.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain S residue 89 THR Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain W residue 21 ILE Chi-restraints excluded: chain W residue 82 ASP Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 40 VAL Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 0.8980 chunk 202 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 140 optimal weight: 9.9990 chunk 212 optimal weight: 10.0000 chunk 195 optimal weight: 0.6980 chunk 168 optimal weight: 3.9990 chunk 17 optimal weight: 10.0000 chunk 130 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN T 55 GLN I 42 GLN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 55 GLN ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.4781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 17412 Z= 0.226 Angle : 0.663 13.102 23586 Z= 0.340 Chirality : 0.047 0.264 2562 Planarity : 0.004 0.054 3057 Dihedral : 4.855 30.258 2523 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.27 % Allowed : 21.74 % Favored : 76.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.18), residues: 2145 helix: 0.44 (0.27), residues: 384 sheet: -1.33 (0.28), residues: 417 loop : -1.72 (0.16), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 111 HIS 0.003 0.001 HIS I 142 PHE 0.014 0.001 PHE X 49 TYR 0.020 0.001 TYR S 58 ARG 0.003 0.000 ARG G 315 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4290 Ramachandran restraints generated. 2145 Oldfield, 0 Emsley, 2145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 190 time to evaluate : 1.895 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: V 53 PHE cc_start: 0.7211 (OUTLIER) cc_final: 0.6076 (m-80) REVERT: V 108 MET cc_start: 0.7294 (tpp) cc_final: 0.6849 (tpp) REVERT: B 17 MET cc_start: 0.6996 (mmm) cc_final: 0.6531 (tpp) REVERT: B 98 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8947 (mm) REVERT: S 53 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.5750 (m-80) REVERT: G 69 TRP cc_start: 0.8650 (OUTLIER) cc_final: 0.8050 (p-90) REVERT: I 17 MET cc_start: 0.6964 (tpp) cc_final: 0.6559 (mpp) REVERT: I 27 GLN cc_start: 0.7743 (tm-30) cc_final: 0.7158 (tm-30) REVERT: I 98 LEU cc_start: 0.9010 (mm) cc_final: 0.8754 (mm) REVERT: U 53 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.5183 (m-80) REVERT: U 81 VAL cc_start: 0.8313 (t) cc_final: 0.7910 (p) REVERT: U 108 MET cc_start: 0.7173 (tpp) cc_final: 0.6589 (tpp) REVERT: U 116 MET cc_start: 0.6547 (mmm) cc_final: 0.6164 (mmm) REVERT: J 27 GLN cc_start: 0.7707 (tm-30) cc_final: 0.7089 (tm-30) REVERT: J 42 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.7916 (tp-100) outliers start: 42 outliers final: 35 residues processed: 226 average time/residue: 0.2411 time to fit residues: 88.0705 Evaluate side-chains 219 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 178 time to evaluate : 1.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain V residue 53 PHE Chi-restraints excluded: chain V residue 67 THR Chi-restraints excluded: chain V residue 89 THR Chi-restraints excluded: chain X residue 21 ILE Chi-restraints excluded: chain A residue 23 THR Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 69 TRP Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 176 VAL Chi-restraints excluded: chain A residue 204 VAL Chi-restraints excluded: chain A residue 256 TYR Chi-restraints excluded: chain B residue 50 ASN Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain S residue 53 PHE Chi-restraints excluded: chain S residue 57 ASN Chi-restraints excluded: chain S residue 67 THR Chi-restraints excluded: chain T residue 21 ILE Chi-restraints excluded: chain T residue 47 LEU Chi-restraints excluded: chain T residue 104 VAL Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 28 THR Chi-restraints excluded: chain G residue 29 VAL Chi-restraints excluded: chain G residue 69 TRP Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 176 VAL Chi-restraints excluded: chain G residue 256 TYR Chi-restraints excluded: chain I residue 50 ASN Chi-restraints excluded: chain I residue 120 GLU Chi-restraints excluded: chain U residue 53 PHE Chi-restraints excluded: chain U residue 67 THR Chi-restraints excluded: chain H residue 23 THR Chi-restraints excluded: chain H residue 28 THR Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 30 LEU Chi-restraints excluded: chain H residue 69 TRP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain H residue 256 TYR Chi-restraints excluded: chain J residue 42 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 155 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 chunk 169 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 173 optimal weight: 0.4980 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** X 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 111 GLN ** B 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** W 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.077018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.065186 restraints weight = 66410.856| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.73 r_work: 0.3386 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17412 Z= 0.285 Angle : 0.682 12.880 23586 Z= 0.348 Chirality : 0.047 0.303 2562 Planarity : 0.004 0.054 3057 Dihedral : 4.895 30.395 2523 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 2.43 % Allowed : 22.01 % Favored : 75.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.18), residues: 2145 helix: 0.46 (0.27), residues: 384 sheet: -1.27 (0.28), residues: 417 loop : -1.68 (0.17), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP V 111 HIS 0.004 0.001 HIS H 184 PHE 0.021 0.002 PHE W 83 TYR 0.022 0.002 TYR V 58 ARG 0.003 0.000 ARG G 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3167.00 seconds wall clock time: 58 minutes 37.34 seconds (3517.34 seconds total)