Starting phenix.real_space_refine on Mon Oct 14 22:34:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/10_2024/7rsl_24674.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/10_2024/7rsl_24674.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/10_2024/7rsl_24674.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/10_2024/7rsl_24674.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/10_2024/7rsl_24674.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rsl_24674/10_2024/7rsl_24674.cif" } resolution = 3.45 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 90 5.16 5 C 12460 2.51 5 N 3120 2.21 5 O 3480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 19150 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "B" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "G" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "H" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "E" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "F" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "I" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "J" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "C" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Chain: "D" Number of atoms: 1915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1915 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 11, 'TRANS': 223} Chain breaks: 1 Time building chain proxies: 11.29, per 1000 atoms: 0.59 Number of scatterers: 19150 At special positions: 0 Unit cell: (155.925, 154.275, 85.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 90 16.00 O 3480 8.00 N 3120 7.00 C 12460 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.97 Conformation dependent library (CDL) restraints added in 2.5 seconds 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4520 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 40 sheets defined 34.7% alpha, 37.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.47 Creating SS restraints... Processing helix chain 'A' and resid 18 through 45 Proline residue: A 31 - end of helix Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 174 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE A 252 " --> pdb=" O TYR A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 45 Proline residue: B 31 - end of helix Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 174 Processing helix chain 'B' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU B 187 " --> pdb=" O ASP B 183 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 45 Proline residue: G 31 - end of helix Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 174 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'G' and resid 234 through 243 Processing helix chain 'G' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE G 252 " --> pdb=" O TYR G 248 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 45 Proline residue: H 31 - end of helix Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 174 Processing helix chain 'H' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU H 187 " --> pdb=" O ASP H 183 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU H 246 " --> pdb=" O ARG H 242 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 45 Proline residue: E 31 - end of helix Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 174 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'E' and resid 234 through 243 Processing helix chain 'E' and resid 243 through 264 removed outlier: 3.857A pdb=" N ILE E 252 " --> pdb=" O TYR E 248 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 45 Proline residue: F 31 - end of helix Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 174 Processing helix chain 'F' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU F 187 " --> pdb=" O ASP F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU F 246 " --> pdb=" O ARG F 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 45 Proline residue: I 31 - end of helix Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 174 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'I' and resid 234 through 243 Processing helix chain 'I' and resid 243 through 264 removed outlier: 3.856A pdb=" N ILE I 252 " --> pdb=" O TYR I 248 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 45 Proline residue: J 31 - end of helix Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 174 Processing helix chain 'J' and resid 177 through 187 removed outlier: 3.728A pdb=" N LEU J 187 " --> pdb=" O ASP J 183 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 264 removed outlier: 3.610A pdb=" N LEU J 246 " --> pdb=" O ARG J 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 45 Proline residue: C 31 - end of helix Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'C' and resid 234 through 243 Processing helix chain 'C' and resid 243 through 264 removed outlier: 3.856A pdb=" N ILE C 252 " --> pdb=" O TYR C 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 45 Proline residue: D 31 - end of helix Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 177 through 187 removed outlier: 3.729A pdb=" N LEU D 187 " --> pdb=" O ASP D 183 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 264 removed outlier: 3.611A pdb=" N LEU D 246 " --> pdb=" O ARG D 242 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE A 196 " --> pdb=" O LEU A 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU A 107 " --> pdb=" O ASP A 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP A 194 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU A 109 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE A 192 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU A 111 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE A 190 " --> pdb=" O LEU A 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS A 113 " --> pdb=" O ASN A 188 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ASN A 188 " --> pdb=" O CYS A 113 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE A 71 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 205 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR A 204 " --> pdb=" O GLY A 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 132 " --> pdb=" O THR A 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG A 131 " --> pdb=" O LYS A 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS A 149 " --> pdb=" O ARG A 131 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.878A pdb=" N MET A 97 " --> pdb=" O LYS A 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR B 103 " --> pdb=" O ILE B 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE B 196 " --> pdb=" O TYR B 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU B 105 " --> pdb=" O ASP B 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP B 194 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 54 Processing sheet with id=AA7, first strand: chain 'B' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER B 206 " --> pdb=" O TYR B 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG B 131 " --> pdb=" O LYS B 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS B 149 " --> pdb=" O ARG B 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 74 through 76 Processing sheet with id=AA9, first strand: chain 'G' and resid 51 through 54 removed outlier: 4.665A pdb=" N ILE G 196 " --> pdb=" O LEU G 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU G 107 " --> pdb=" O ASP G 194 " (cutoff:3.500A) removed outlier: 7.669A pdb=" N ASP G 194 " --> pdb=" O LEU G 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU G 109 " --> pdb=" O ILE G 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE G 192 " --> pdb=" O LEU G 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU G 111 " --> pdb=" O ILE G 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE G 190 " --> pdb=" O LEU G 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS G 113 " --> pdb=" O ASN G 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN G 188 " --> pdb=" O CYS G 113 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 51 through 54 Processing sheet with id=AB2, first strand: chain 'G' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE G 71 " --> pdb=" O ASN G 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE G 205 " --> pdb=" O GLN G 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR G 204 " --> pdb=" O GLY G 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY G 132 " --> pdb=" O THR G 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG G 131 " --> pdb=" O LYS G 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS G 149 " --> pdb=" O ARG G 131 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.823A pdb=" N MET G 97 " --> pdb=" O LYS G 75 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR H 103 " --> pdb=" O ILE H 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE H 196 " --> pdb=" O TYR H 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU H 105 " --> pdb=" O ASP H 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP H 194 " --> pdb=" O LEU H 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 50 through 54 Processing sheet with id=AB6, first strand: chain 'H' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER H 206 " --> pdb=" O TYR H 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG H 131 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS H 149 " --> pdb=" O ARG H 131 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 74 through 76 Processing sheet with id=AB8, first strand: chain 'E' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE E 196 " --> pdb=" O LEU E 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU E 107 " --> pdb=" O ASP E 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP E 194 " --> pdb=" O LEU E 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU E 109 " --> pdb=" O ILE E 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE E 192 " --> pdb=" O LEU E 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU E 111 " --> pdb=" O ILE E 190 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE E 190 " --> pdb=" O LEU E 111 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS E 113 " --> pdb=" O ASN E 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN E 188 " --> pdb=" O CYS E 113 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 51 through 54 Processing sheet with id=AC1, first strand: chain 'E' and resid 59 through 61 removed outlier: 3.618A pdb=" N PHE E 71 " --> pdb=" O ASN E 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE E 205 " --> pdb=" O GLN E 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR E 204 " --> pdb=" O GLY E 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY E 132 " --> pdb=" O THR E 204 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG E 131 " --> pdb=" O LYS E 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS E 149 " --> pdb=" O ARG E 131 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.823A pdb=" N MET E 97 " --> pdb=" O LYS E 75 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR F 103 " --> pdb=" O ILE F 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE F 196 " --> pdb=" O TYR F 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU F 105 " --> pdb=" O ASP F 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP F 194 " --> pdb=" O LEU F 105 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 50 through 54 Processing sheet with id=AC5, first strand: chain 'F' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER F 206 " --> pdb=" O TYR F 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG F 131 " --> pdb=" O LYS F 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS F 149 " --> pdb=" O ARG F 131 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 74 through 76 Processing sheet with id=AC7, first strand: chain 'I' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE I 196 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N LEU I 107 " --> pdb=" O ASP I 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP I 194 " --> pdb=" O LEU I 107 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU I 109 " --> pdb=" O ILE I 192 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE I 192 " --> pdb=" O LEU I 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU I 111 " --> pdb=" O ILE I 190 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N ILE I 190 " --> pdb=" O LEU I 111 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N CYS I 113 " --> pdb=" O ASN I 188 " (cutoff:3.500A) removed outlier: 8.893A pdb=" N ASN I 188 " --> pdb=" O CYS I 113 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 51 through 54 Processing sheet with id=AC9, first strand: chain 'I' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE I 71 " --> pdb=" O ASN I 59 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE I 205 " --> pdb=" O GLN I 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR I 204 " --> pdb=" O GLY I 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY I 132 " --> pdb=" O THR I 204 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ARG I 131 " --> pdb=" O LYS I 149 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N LYS I 149 " --> pdb=" O ARG I 131 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 74 through 77 removed outlier: 3.877A pdb=" N MET I 97 " --> pdb=" O LYS I 75 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 50 through 54 removed outlier: 7.216A pdb=" N TYR J 103 " --> pdb=" O ILE J 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE J 196 " --> pdb=" O TYR J 103 " (cutoff:3.500A) removed outlier: 7.683A pdb=" N LEU J 105 " --> pdb=" O ASP J 194 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ASP J 194 " --> pdb=" O LEU J 105 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 50 through 54 Processing sheet with id=AD4, first strand: chain 'J' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER J 206 " --> pdb=" O TYR J 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG J 131 " --> pdb=" O LYS J 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS J 149 " --> pdb=" O ARG J 131 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'J' and resid 74 through 76 Processing sheet with id=AD6, first strand: chain 'C' and resid 51 through 54 removed outlier: 4.666A pdb=" N ILE C 196 " --> pdb=" O LEU C 105 " (cutoff:3.500A) removed outlier: 9.004A pdb=" N LEU C 107 " --> pdb=" O ASP C 194 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N ASP C 194 " --> pdb=" O LEU C 107 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N LEU C 109 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N ILE C 192 " --> pdb=" O LEU C 109 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N LEU C 111 " --> pdb=" O ILE C 190 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ILE C 190 " --> pdb=" O LEU C 111 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N CYS C 113 " --> pdb=" O ASN C 188 " (cutoff:3.500A) removed outlier: 8.892A pdb=" N ASN C 188 " --> pdb=" O CYS C 113 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 51 through 54 Processing sheet with id=AD8, first strand: chain 'C' and resid 59 through 61 removed outlier: 3.617A pdb=" N PHE C 71 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE C 205 " --> pdb=" O GLN C 72 " (cutoff:3.500A) removed outlier: 5.184A pdb=" N THR C 204 " --> pdb=" O GLY C 132 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY C 132 " --> pdb=" O THR C 204 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N ARG C 131 " --> pdb=" O LYS C 149 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LYS C 149 " --> pdb=" O ARG C 131 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.878A pdb=" N MET C 97 " --> pdb=" O LYS C 75 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 50 through 54 removed outlier: 7.215A pdb=" N TYR D 103 " --> pdb=" O ILE D 196 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ILE D 196 " --> pdb=" O TYR D 103 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N LEU D 105 " --> pdb=" O ASP D 194 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP D 194 " --> pdb=" O LEU D 105 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 50 through 54 Processing sheet with id=AE3, first strand: chain 'D' and resid 59 through 61 removed outlier: 3.569A pdb=" N SER D 206 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ARG D 131 " --> pdb=" O LYS D 149 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N LYS D 149 " --> pdb=" O ARG D 131 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 74 through 76 1070 hydrogen bonds defined for protein. 2985 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: 6.34 Time building geometry restraints manager: 5.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4854 1.33 - 1.45: 3393 1.45 - 1.57: 11153 1.57 - 1.69: 0 1.69 - 1.81: 140 Bond restraints: 19540 Sorted by residual: bond pdb=" N ILE B 150 " pdb=" CA ILE B 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE J 150 " pdb=" CA ILE J 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE H 150 " pdb=" CA ILE H 150 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.06e-02 8.90e+03 1.26e+01 bond pdb=" N ILE D 150 " pdb=" CA ILE D 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.25e+01 bond pdb=" N ILE F 150 " pdb=" CA ILE F 150 " ideal model delta sigma weight residual 1.455 1.492 -0.037 1.06e-02 8.90e+03 1.24e+01 ... (remaining 19535 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 25402 1.97 - 3.93: 972 3.93 - 5.90: 105 5.90 - 7.86: 6 7.86 - 9.83: 5 Bond angle restraints: 26490 Sorted by residual: angle pdb=" N HIS J 119 " pdb=" CA HIS J 119 " pdb=" C HIS J 119 " ideal model delta sigma weight residual 110.50 100.67 9.83 1.41e+00 5.03e-01 4.86e+01 angle pdb=" N HIS H 119 " pdb=" CA HIS H 119 " pdb=" C HIS H 119 " ideal model delta sigma weight residual 110.50 100.70 9.80 1.41e+00 5.03e-01 4.83e+01 angle pdb=" N HIS B 119 " pdb=" CA HIS B 119 " pdb=" C HIS B 119 " ideal model delta sigma weight residual 110.50 100.73 9.77 1.41e+00 5.03e-01 4.80e+01 angle pdb=" N HIS D 119 " pdb=" CA HIS D 119 " pdb=" C HIS D 119 " ideal model delta sigma weight residual 110.50 100.73 9.77 1.41e+00 5.03e-01 4.80e+01 angle pdb=" N HIS F 119 " pdb=" CA HIS F 119 " pdb=" C HIS F 119 " ideal model delta sigma weight residual 110.50 100.76 9.74 1.41e+00 5.03e-01 4.77e+01 ... (remaining 26485 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 10796 17.74 - 35.48: 872 35.48 - 53.22: 119 53.22 - 70.96: 47 70.96 - 88.70: 16 Dihedral angle restraints: 11850 sinusoidal: 4910 harmonic: 6940 Sorted by residual: dihedral pdb=" CA MET J 101 " pdb=" C MET J 101 " pdb=" N GLU J 102 " pdb=" CA GLU J 102 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET D 101 " pdb=" C MET D 101 " pdb=" N GLU D 102 " pdb=" CA GLU D 102 " ideal model delta harmonic sigma weight residual -180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA MET B 101 " pdb=" C MET B 101 " pdb=" N GLU B 102 " pdb=" CA GLU B 102 " ideal model delta harmonic sigma weight residual 180.00 -154.72 -25.28 0 5.00e+00 4.00e-02 2.56e+01 ... (remaining 11847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2091 0.041 - 0.082: 623 0.082 - 0.122: 315 0.122 - 0.163: 60 0.163 - 0.204: 21 Chirality restraints: 3110 Sorted by residual: chirality pdb=" CA LEU J 91 " pdb=" N LEU J 91 " pdb=" C LEU J 91 " pdb=" CB LEU J 91 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA ILE G 28 " pdb=" N ILE G 28 " pdb=" C ILE G 28 " pdb=" CB ILE G 28 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CA ILE D 205 " pdb=" N ILE D 205 " pdb=" C ILE D 205 " pdb=" CB ILE D 205 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.71e-01 ... (remaining 3107 not shown) Planarity restraints: 3340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP H 118 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.56e+00 pdb=" CG ASP H 118 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP H 118 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP H 118 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP J 118 " -0.013 2.00e-02 2.50e+03 2.55e-02 6.52e+00 pdb=" CG ASP J 118 " 0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP J 118 " -0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP J 118 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP D 118 " 0.012 2.00e-02 2.50e+03 2.55e-02 6.48e+00 pdb=" CG ASP D 118 " -0.044 2.00e-02 2.50e+03 pdb=" OD1 ASP D 118 " 0.016 2.00e-02 2.50e+03 pdb=" OD2 ASP D 118 " 0.015 2.00e-02 2.50e+03 ... (remaining 3337 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1643 2.74 - 3.28: 19652 3.28 - 3.82: 30021 3.82 - 4.36: 37019 4.36 - 4.90: 64414 Nonbonded interactions: 152749 Sorted by model distance: nonbonded pdb=" OD1 ASP I 194 " pdb=" NH2 ARG I 229 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASP C 194 " pdb=" NH2 ARG C 229 " model vdw 2.200 3.120 nonbonded pdb=" OD1 ASP A 194 " pdb=" NH2 ARG A 229 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP E 194 " pdb=" NH2 ARG E 229 " model vdw 2.201 3.120 nonbonded pdb=" OD1 ASP G 194 " pdb=" NH2 ARG G 229 " model vdw 2.202 3.120 ... (remaining 152744 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 2.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 44.070 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.110 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.007 0.041 19540 Z= 0.454 Angle : 0.818 9.828 26490 Z= 0.528 Chirality : 0.051 0.204 3110 Planarity : 0.005 0.043 3340 Dihedral : 13.619 88.702 7330 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 11.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.23 % Allowed : 1.71 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.17), residues: 2310 helix: 0.67 (0.19), residues: 725 sheet: -2.21 (0.18), residues: 735 loop : -1.63 (0.20), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP F 186 HIS 0.005 0.001 HIS F 152 PHE 0.017 0.002 PHE E 40 TYR 0.019 0.002 TYR G 103 ARG 0.013 0.001 ARG C 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 520 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 515 time to evaluate : 2.317 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8922 (mmmt) cc_final: 0.8706 (mmtt) REVERT: A 173 GLN cc_start: 0.8963 (mt0) cc_final: 0.8647 (mt0) REVERT: B 104 LYS cc_start: 0.9269 (ttmm) cc_final: 0.8960 (tptp) REVERT: B 184 GLU cc_start: 0.8644 (mm-30) cc_final: 0.8247 (mm-30) REVERT: B 212 GLU cc_start: 0.8465 (tt0) cc_final: 0.8262 (tt0) REVERT: B 227 LYS cc_start: 0.9394 (mtpt) cc_final: 0.9175 (ttmm) REVERT: G 173 GLN cc_start: 0.8534 (mt0) cc_final: 0.8048 (mt0) REVERT: H 104 LYS cc_start: 0.9281 (ttmm) cc_final: 0.8962 (tptp) REVERT: H 184 GLU cc_start: 0.8642 (mm-30) cc_final: 0.8284 (mm-30) REVERT: E 173 GLN cc_start: 0.7977 (mt0) cc_final: 0.7383 (mt0) REVERT: E 202 TYR cc_start: 0.8810 (m-80) cc_final: 0.8502 (m-80) REVERT: F 103 TYR cc_start: 0.8091 (m-80) cc_final: 0.7859 (m-80) REVERT: F 183 ASP cc_start: 0.8909 (t70) cc_final: 0.8693 (t0) REVERT: F 184 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8254 (mm-30) REVERT: F 195 LYS cc_start: 0.9268 (mmtp) cc_final: 0.8968 (mmmm) REVERT: F 212 GLU cc_start: 0.8506 (tt0) cc_final: 0.8292 (tt0) REVERT: F 227 LYS cc_start: 0.9395 (mtpt) cc_final: 0.9178 (tppp) REVERT: F 234 GLN cc_start: 0.9588 (mm-40) cc_final: 0.9354 (tp40) REVERT: I 97 MET cc_start: 0.7895 (ptm) cc_final: 0.7639 (ptm) REVERT: I 202 TYR cc_start: 0.8316 (m-80) cc_final: 0.8083 (m-80) REVERT: J 104 LYS cc_start: 0.9230 (ttmm) cc_final: 0.9000 (tptp) REVERT: J 184 GLU cc_start: 0.8688 (mm-30) cc_final: 0.8284 (mm-30) REVERT: C 173 GLN cc_start: 0.8167 (mt0) cc_final: 0.7705 (mt0) REVERT: D 104 LYS cc_start: 0.9230 (ttmm) cc_final: 0.8925 (tptp) REVERT: D 184 GLU cc_start: 0.8635 (mm-30) cc_final: 0.8409 (mm-30) REVERT: D 195 LYS cc_start: 0.9239 (mmtp) cc_final: 0.8978 (mmmm) REVERT: D 212 GLU cc_start: 0.8554 (tt0) cc_final: 0.8173 (tt0) REVERT: D 227 LYS cc_start: 0.9424 (mtpt) cc_final: 0.9203 (ttmm) outliers start: 5 outliers final: 0 residues processed: 515 average time/residue: 0.3401 time to fit residues: 263.1975 Evaluate side-chains 308 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 2.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 194 optimal weight: 10.0000 chunk 174 optimal weight: 4.9990 chunk 96 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 93 optimal weight: 30.0000 chunk 180 optimal weight: 5.9990 chunk 69 optimal weight: 7.9990 chunk 109 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 208 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 121 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN G 93 GLN G 121 ASN H 114 GLN ** H 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN E 121 ASN F 114 GLN F 119 HIS I 93 GLN I 121 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN C 114 GLN C 121 ASN D 114 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19540 Z= 0.270 Angle : 0.650 11.421 26490 Z= 0.331 Chirality : 0.044 0.157 3110 Planarity : 0.005 0.048 3340 Dihedral : 4.879 23.793 2530 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.26 % Allowed : 11.71 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.14 (0.18), residues: 2310 helix: 0.93 (0.19), residues: 740 sheet: -1.65 (0.18), residues: 835 loop : -1.12 (0.24), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 186 HIS 0.003 0.001 HIS F 119 PHE 0.012 0.001 PHE J 228 TYR 0.022 0.002 TYR G 37 ARG 0.008 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 328 time to evaluate : 2.358 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: symmetry clash revert: symmetry clash REVERT: B 116 LYS cc_start: 0.8912 (mppt) cc_final: 0.8608 (mttp) REVERT: B 172 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7535 (mt-10) REVERT: B 195 LYS cc_start: 0.8970 (mmmm) cc_final: 0.8345 (mmmm) REVERT: B 227 LYS cc_start: 0.9455 (mtpt) cc_final: 0.9227 (ttmm) REVERT: G 101 MET cc_start: 0.8377 (tpt) cc_final: 0.7654 (tpp) REVERT: G 173 GLN cc_start: 0.8749 (mt0) cc_final: 0.8428 (mt0) REVERT: H 130 TYR cc_start: 0.9041 (m-10) cc_final: 0.8731 (m-10) REVERT: H 195 LYS cc_start: 0.8810 (mmmm) cc_final: 0.8086 (mmmm) REVERT: E 88 ASP cc_start: 0.8392 (p0) cc_final: 0.8102 (p0) REVERT: E 172 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8622 (tm-30) REVERT: E 173 GLN cc_start: 0.8659 (mt0) cc_final: 0.8184 (mt0) REVERT: E 202 TYR cc_start: 0.8821 (m-80) cc_final: 0.8463 (m-80) REVERT: F 17 TYR cc_start: 0.6056 (p90) cc_final: 0.5595 (p90) REVERT: F 172 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7936 (mt-10) REVERT: I 230 MET cc_start: 0.8741 (tmm) cc_final: 0.8461 (tmm) REVERT: J 172 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7622 (mt-10) REVERT: C 88 ASP cc_start: 0.8351 (p0) cc_final: 0.7983 (p0) REVERT: C 173 GLN cc_start: 0.8670 (mt0) cc_final: 0.7993 (mt0) REVERT: C 202 TYR cc_start: 0.8825 (m-80) cc_final: 0.8465 (m-80) REVERT: C 230 MET cc_start: 0.8888 (tmm) cc_final: 0.8538 (tmm) REVERT: D 172 GLU cc_start: 0.8256 (mt-10) cc_final: 0.7991 (tt0) REVERT: D 195 LYS cc_start: 0.9029 (mmtp) cc_final: 0.8809 (mmmm) REVERT: D 212 GLU cc_start: 0.8500 (tt0) cc_final: 0.8167 (tt0) outliers start: 28 outliers final: 14 residues processed: 345 average time/residue: 0.3178 time to fit residues: 166.5198 Evaluate side-chains 293 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 279 time to evaluate : 2.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 116 optimal weight: 9.9990 chunk 64 optimal weight: 9.9990 chunk 173 optimal weight: 3.9990 chunk 142 optimal weight: 8.9990 chunk 57 optimal weight: 5.9990 chunk 209 optimal weight: 6.9990 chunk 226 optimal weight: 5.9990 chunk 186 optimal weight: 20.0000 chunk 207 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 167 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 119 HIS H 121 ASN F 119 HIS ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 19540 Z= 0.423 Angle : 0.669 11.146 26490 Z= 0.336 Chirality : 0.043 0.144 3110 Planarity : 0.004 0.043 3340 Dihedral : 4.865 21.242 2530 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.39 % Allowed : 13.96 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.17), residues: 2310 helix: 0.98 (0.18), residues: 740 sheet: -1.37 (0.17), residues: 865 loop : -1.15 (0.23), residues: 705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 186 HIS 0.007 0.001 HIS H 38 PHE 0.011 0.001 PHE B 228 TYR 0.021 0.002 TYR F 103 ARG 0.007 0.001 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 250 time to evaluate : 2.477 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: B 116 LYS cc_start: 0.8871 (mppt) cc_final: 0.8532 (mttp) REVERT: B 227 LYS cc_start: 0.9487 (mtpt) cc_final: 0.9237 (ttmm) REVERT: G 88 ASP cc_start: 0.8662 (p0) cc_final: 0.8392 (p0) REVERT: G 100 ASN cc_start: 0.8431 (m-40) cc_final: 0.8097 (m110) REVERT: H 130 TYR cc_start: 0.9111 (m-10) cc_final: 0.8750 (m-10) REVERT: E 88 ASP cc_start: 0.8534 (p0) cc_final: 0.8317 (p0) REVERT: E 116 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8458 (tptt) REVERT: F 17 TYR cc_start: 0.6136 (p90) cc_final: 0.5621 (p90) REVERT: F 169 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8284 (tp-100) REVERT: F 172 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7954 (mt-10) REVERT: F 173 GLN cc_start: 0.8942 (mt0) cc_final: 0.8643 (mt0) REVERT: F 184 GLU cc_start: 0.8858 (tp30) cc_final: 0.8512 (mm-30) REVERT: F 195 LYS cc_start: 0.9139 (mmmm) cc_final: 0.8879 (mmmm) REVERT: I 202 TYR cc_start: 0.8491 (m-80) cc_final: 0.8225 (m-80) REVERT: I 230 MET cc_start: 0.8801 (tmm) cc_final: 0.8455 (tmm) REVERT: C 88 ASP cc_start: 0.8546 (p0) cc_final: 0.8268 (p0) REVERT: C 230 MET cc_start: 0.8985 (tmm) cc_final: 0.8412 (tmm) REVERT: D 195 LYS cc_start: 0.9122 (mmtp) cc_final: 0.8815 (mmmm) outliers start: 53 outliers final: 33 residues processed: 276 average time/residue: 0.3499 time to fit residues: 146.8737 Evaluate side-chains 274 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 241 time to evaluate : 2.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 230 MET Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 165 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 206 optimal weight: 30.0000 chunk 157 optimal weight: 3.9990 chunk 108 optimal weight: 2.9990 chunk 23 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 209 optimal weight: 9.9990 chunk 222 optimal weight: 0.8980 chunk 109 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 59 optimal weight: 0.0030 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 19540 Z= 0.204 Angle : 0.575 8.626 26490 Z= 0.288 Chirality : 0.042 0.144 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.480 19.382 2530 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.80 % Allowed : 16.04 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.18), residues: 2310 helix: 1.26 (0.19), residues: 740 sheet: -1.11 (0.17), residues: 845 loop : -0.84 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP F 186 HIS 0.010 0.001 HIS E 119 PHE 0.011 0.001 PHE D 40 TYR 0.020 0.002 TYR D 103 ARG 0.004 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 279 time to evaluate : 2.373 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: symmetry clash revert: symmetry clash REVERT: A 116 LYS cc_start: 0.8880 (mmmt) cc_final: 0.8614 (tptt) REVERT: B 116 LYS cc_start: 0.8882 (mppt) cc_final: 0.8557 (mttp) REVERT: B 172 GLU cc_start: 0.7989 (mt-10) cc_final: 0.7541 (mt-10) REVERT: G 88 ASP cc_start: 0.8639 (p0) cc_final: 0.8430 (p0) REVERT: G 116 LYS cc_start: 0.8583 (tptt) cc_final: 0.8330 (mmmt) REVERT: G 202 TYR cc_start: 0.8646 (m-80) cc_final: 0.8313 (m-10) REVERT: H 130 TYR cc_start: 0.9065 (m-10) cc_final: 0.8714 (m-10) REVERT: H 184 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8187 (mm-30) REVERT: H 195 LYS cc_start: 0.8782 (mmmm) cc_final: 0.8538 (mmmm) REVERT: H 227 LYS cc_start: 0.9353 (ttmm) cc_final: 0.9069 (tptp) REVERT: E 88 ASP cc_start: 0.8500 (p0) cc_final: 0.8222 (p0) REVERT: E 116 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8429 (tptt) REVERT: E 202 TYR cc_start: 0.8632 (m-80) cc_final: 0.8252 (m-80) REVERT: F 17 TYR cc_start: 0.6162 (p90) cc_final: 0.5606 (p90) REVERT: F 103 TYR cc_start: 0.8382 (m-80) cc_final: 0.7928 (m-10) REVERT: F 169 GLN cc_start: 0.8621 (tp-100) cc_final: 0.8168 (tp-100) REVERT: F 173 GLN cc_start: 0.8868 (mt0) cc_final: 0.8394 (mt0) REVERT: F 184 GLU cc_start: 0.8789 (tp30) cc_final: 0.8509 (mm-30) REVERT: F 195 LYS cc_start: 0.9213 (mmmm) cc_final: 0.8928 (mmmm) REVERT: I 202 TYR cc_start: 0.8409 (m-80) cc_final: 0.8167 (m-80) REVERT: I 230 MET cc_start: 0.8746 (tmm) cc_final: 0.8416 (tmm) REVERT: J 172 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7665 (mt-10) REVERT: C 88 ASP cc_start: 0.8499 (p0) cc_final: 0.8175 (p0) REVERT: C 173 GLN cc_start: 0.8382 (mt0) cc_final: 0.8117 (mt0) REVERT: C 230 MET cc_start: 0.9010 (tmm) cc_final: 0.8421 (tmm) REVERT: D 195 LYS cc_start: 0.8945 (mmtp) cc_final: 0.8630 (mmmm) REVERT: D 212 GLU cc_start: 0.8466 (tt0) cc_final: 0.8102 (tt0) REVERT: D 227 LYS cc_start: 0.9465 (ttmm) cc_final: 0.9017 (tttp) outliers start: 40 outliers final: 24 residues processed: 298 average time/residue: 0.3252 time to fit residues: 146.9455 Evaluate side-chains 288 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 264 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 165 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 185 optimal weight: 40.0000 chunk 126 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 165 optimal weight: 9.9990 chunk 91 optimal weight: 6.9990 chunk 189 optimal weight: 0.9990 chunk 153 optimal weight: 5.9990 chunk 0 optimal weight: 50.0000 chunk 113 optimal weight: 5.9990 chunk 199 optimal weight: 7.9990 chunk 56 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 HIS ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 119 HIS E 173 GLN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 173 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 93 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 19540 Z= 0.309 Angle : 0.604 11.570 26490 Z= 0.300 Chirality : 0.042 0.143 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.446 18.741 2530 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.39 % Allowed : 17.03 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.18), residues: 2310 helix: 1.32 (0.19), residues: 745 sheet: -0.97 (0.17), residues: 870 loop : -0.98 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 186 HIS 0.010 0.001 HIS J 38 PHE 0.010 0.001 PHE F 40 TYR 0.014 0.002 TYR D 103 ARG 0.004 0.000 ARG A 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 272 time to evaluate : 2.386 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: A 40 PHE cc_start: 0.8768 (OUTLIER) cc_final: 0.8550 (m-80) REVERT: A 248 TYR cc_start: 0.8708 (OUTLIER) cc_final: 0.8049 (m-80) REVERT: B 116 LYS cc_start: 0.8888 (mppt) cc_final: 0.8534 (mttp) REVERT: B 130 TYR cc_start: 0.9112 (m-80) cc_final: 0.8558 (m-10) REVERT: B 227 LYS cc_start: 0.9308 (ttmm) cc_final: 0.9064 (tptp) REVERT: G 88 ASP cc_start: 0.8677 (p0) cc_final: 0.8473 (p0) REVERT: G 116 LYS cc_start: 0.8610 (tptt) cc_final: 0.8346 (tptt) REVERT: G 117 THR cc_start: 0.9144 (p) cc_final: 0.8479 (p) REVERT: G 166 MET cc_start: 0.8556 (OUTLIER) cc_final: 0.8348 (mpp) REVERT: G 202 TYR cc_start: 0.8659 (m-80) cc_final: 0.8450 (m-80) REVERT: H 130 TYR cc_start: 0.9098 (m-10) cc_final: 0.8729 (m-10) REVERT: H 184 GLU cc_start: 0.8770 (mm-30) cc_final: 0.8231 (mm-30) REVERT: H 195 LYS cc_start: 0.8883 (mmmm) cc_final: 0.8626 (mmmm) REVERT: E 42 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8735 (pp) REVERT: E 88 ASP cc_start: 0.8566 (p0) cc_final: 0.8278 (p0) REVERT: E 230 MET cc_start: 0.9262 (tpp) cc_final: 0.8913 (tpp) REVERT: E 248 TYR cc_start: 0.8772 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: F 17 TYR cc_start: 0.6196 (p90) cc_final: 0.5651 (p90) REVERT: F 104 LYS cc_start: 0.9245 (OUTLIER) cc_final: 0.8881 (mmmt) REVERT: F 169 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8206 (tp-100) REVERT: F 173 GLN cc_start: 0.8867 (mt0) cc_final: 0.8249 (mt0) REVERT: F 184 GLU cc_start: 0.8832 (tp30) cc_final: 0.8585 (mm-30) REVERT: F 194 ASP cc_start: 0.8384 (t0) cc_final: 0.8136 (m-30) REVERT: F 195 LYS cc_start: 0.9272 (mmmm) cc_final: 0.8932 (mmmm) REVERT: I 202 TYR cc_start: 0.8494 (m-80) cc_final: 0.8219 (m-80) REVERT: I 230 MET cc_start: 0.8682 (tmm) cc_final: 0.8239 (tmm) REVERT: J 122 LEU cc_start: 0.9498 (tp) cc_final: 0.9282 (mp) REVERT: C 88 ASP cc_start: 0.8558 (p0) cc_final: 0.8210 (p0) REVERT: C 100 ASN cc_start: 0.8293 (m-40) cc_final: 0.8069 (m110) REVERT: C 202 TYR cc_start: 0.8864 (m-80) cc_final: 0.8589 (m-80) REVERT: C 230 MET cc_start: 0.9030 (tmm) cc_final: 0.8354 (tmm) REVERT: D 184 GLU cc_start: 0.8731 (mm-30) cc_final: 0.8292 (mm-30) REVERT: D 195 LYS cc_start: 0.8976 (mmtp) cc_final: 0.8632 (mmmm) REVERT: D 212 GLU cc_start: 0.8515 (tt0) cc_final: 0.8141 (tt0) outliers start: 53 outliers final: 33 residues processed: 299 average time/residue: 0.3200 time to fit residues: 144.7815 Evaluate side-chains 298 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 259 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 74 optimal weight: 6.9990 chunk 200 optimal weight: 6.9990 chunk 43 optimal weight: 8.9990 chunk 130 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 222 optimal weight: 1.9990 chunk 184 optimal weight: 50.0000 chunk 103 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN G 119 HIS H 72 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 72 GLN I 100 ASN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 19540 Z= 0.286 Angle : 0.610 11.331 26490 Z= 0.302 Chirality : 0.042 0.146 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.380 18.419 2530 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.84 % Allowed : 17.34 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2310 helix: 1.40 (0.19), residues: 745 sheet: -0.80 (0.17), residues: 870 loop : -0.91 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 186 HIS 0.011 0.001 HIS A 119 PHE 0.010 0.001 PHE D 40 TYR 0.014 0.001 TYR G 130 ARG 0.004 0.000 ARG G 229 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 283 time to evaluate : 2.458 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.8776 (OUTLIER) cc_final: 0.8559 (m-80) REVERT: A 100 ASN cc_start: 0.8463 (m-40) cc_final: 0.8248 (m110) REVERT: A 248 TYR cc_start: 0.8750 (OUTLIER) cc_final: 0.8075 (m-80) REVERT: B 116 LYS cc_start: 0.8898 (mppt) cc_final: 0.8540 (mttp) REVERT: B 130 TYR cc_start: 0.9123 (m-80) cc_final: 0.8574 (m-10) REVERT: B 227 LYS cc_start: 0.9317 (ttmm) cc_final: 0.9106 (tptp) REVERT: G 88 ASP cc_start: 0.8683 (p0) cc_final: 0.8482 (p0) REVERT: G 101 MET cc_start: 0.8849 (tpp) cc_final: 0.8472 (tpp) REVERT: G 116 LYS cc_start: 0.8568 (tptt) cc_final: 0.8260 (tptt) REVERT: G 202 TYR cc_start: 0.8667 (m-80) cc_final: 0.8450 (m-80) REVERT: G 248 TYR cc_start: 0.8903 (OUTLIER) cc_final: 0.8100 (m-80) REVERT: H 130 TYR cc_start: 0.9106 (m-10) cc_final: 0.8752 (m-10) REVERT: H 184 GLU cc_start: 0.8779 (mm-30) cc_final: 0.8228 (mm-30) REVERT: H 195 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8636 (mmmm) REVERT: H 227 LYS cc_start: 0.9434 (ttmm) cc_final: 0.9059 (tptp) REVERT: E 42 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8714 (pp) REVERT: E 88 ASP cc_start: 0.8594 (p0) cc_final: 0.8341 (p0) REVERT: E 116 LYS cc_start: 0.8669 (tptt) cc_final: 0.8446 (tptt) REVERT: E 202 TYR cc_start: 0.8678 (m-80) cc_final: 0.8360 (m-80) REVERT: E 230 MET cc_start: 0.9234 (tpp) cc_final: 0.8994 (tpp) REVERT: E 248 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8054 (m-80) REVERT: F 104 LYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8875 (mmmt) REVERT: F 173 GLN cc_start: 0.8809 (mt0) cc_final: 0.8276 (mt0) REVERT: F 194 ASP cc_start: 0.8323 (t0) cc_final: 0.8094 (m-30) REVERT: F 195 LYS cc_start: 0.9286 (mmmm) cc_final: 0.8928 (mmmm) REVERT: I 101 MET cc_start: 0.8492 (tpp) cc_final: 0.8170 (tpp) REVERT: I 202 TYR cc_start: 0.8509 (m-80) cc_final: 0.8238 (m-80) REVERT: I 230 MET cc_start: 0.8589 (tmm) cc_final: 0.8374 (tmm) REVERT: I 248 TYR cc_start: 0.8779 (OUTLIER) cc_final: 0.8067 (m-80) REVERT: J 184 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8219 (mm-30) REVERT: J 193 GLU cc_start: 0.8635 (pm20) cc_final: 0.8398 (pm20) REVERT: J 221 HIS cc_start: 0.9035 (OUTLIER) cc_final: 0.8822 (t-90) REVERT: C 42 LEU cc_start: 0.9053 (mm) cc_final: 0.8684 (pp) REVERT: C 100 ASN cc_start: 0.8343 (m-40) cc_final: 0.8063 (m110) REVERT: C 230 MET cc_start: 0.9022 (tmm) cc_final: 0.8525 (tmm) REVERT: C 248 TYR cc_start: 0.8744 (OUTLIER) cc_final: 0.8026 (m-80) REVERT: D 184 GLU cc_start: 0.8733 (mm-30) cc_final: 0.8480 (tp30) REVERT: D 212 GLU cc_start: 0.8517 (tt0) cc_final: 0.8134 (tt0) REVERT: D 227 LYS cc_start: 0.9463 (ttmm) cc_final: 0.9006 (tttp) outliers start: 63 outliers final: 36 residues processed: 315 average time/residue: 0.3279 time to fit residues: 156.6443 Evaluate side-chains 296 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 251 time to evaluate : 2.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 40 PHE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 166 MET Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 40 PHE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 214 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 126 optimal weight: 7.9990 chunk 162 optimal weight: 7.9990 chunk 125 optimal weight: 5.9990 chunk 187 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 221 optimal weight: 6.9990 chunk 138 optimal weight: 50.0000 chunk 135 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 ASN H 72 GLN E 93 GLN ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 173 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 19540 Z= 0.408 Angle : 0.665 13.086 26490 Z= 0.330 Chirality : 0.043 0.153 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.556 18.171 2530 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.24 % Allowed : 16.98 % Favored : 79.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.18), residues: 2310 helix: 1.28 (0.19), residues: 745 sheet: -0.71 (0.17), residues: 870 loop : -0.96 (0.24), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP I 186 HIS 0.016 0.002 HIS I 119 PHE 0.010 0.001 PHE D 40 TYR 0.013 0.002 TYR G 130 ARG 0.003 0.000 ARG G 229 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 249 time to evaluate : 2.327 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: symmetry clash REVERT: A 40 PHE cc_start: 0.8901 (OUTLIER) cc_final: 0.8691 (m-80) REVERT: A 100 ASN cc_start: 0.8487 (m-40) cc_final: 0.8279 (m110) REVERT: A 101 MET cc_start: 0.8901 (tpp) cc_final: 0.8682 (tpp) REVERT: A 248 TYR cc_start: 0.8768 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: B 116 LYS cc_start: 0.8862 (mppt) cc_final: 0.8495 (mttp) REVERT: B 227 LYS cc_start: 0.9332 (ttmm) cc_final: 0.9101 (tptp) REVERT: G 88 ASP cc_start: 0.8716 (p0) cc_final: 0.8508 (p0) REVERT: G 116 LYS cc_start: 0.8709 (tptt) cc_final: 0.8450 (tptt) REVERT: G 172 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8559 (tt0) REVERT: G 248 TYR cc_start: 0.8910 (OUTLIER) cc_final: 0.8073 (m-80) REVERT: H 184 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8275 (mm-30) REVERT: H 195 LYS cc_start: 0.8963 (mmmm) cc_final: 0.8736 (mmmm) REVERT: H 227 LYS cc_start: 0.9444 (ttmm) cc_final: 0.9013 (tptp) REVERT: E 42 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8753 (pp) REVERT: E 88 ASP cc_start: 0.8628 (p0) cc_final: 0.8394 (p0) REVERT: E 101 MET cc_start: 0.8915 (tpp) cc_final: 0.8528 (tpp) REVERT: E 248 TYR cc_start: 0.8783 (OUTLIER) cc_final: 0.8034 (m-80) REVERT: F 104 LYS cc_start: 0.9181 (OUTLIER) cc_final: 0.8872 (mmmt) REVERT: F 194 ASP cc_start: 0.8359 (t0) cc_final: 0.8135 (m-30) REVERT: F 195 LYS cc_start: 0.9324 (mmmm) cc_final: 0.8969 (mmmm) REVERT: I 101 MET cc_start: 0.8515 (tpp) cc_final: 0.8072 (tpp) REVERT: I 116 LYS cc_start: 0.8529 (tptt) cc_final: 0.8312 (tptt) REVERT: I 248 TYR cc_start: 0.8785 (OUTLIER) cc_final: 0.8068 (m-80) REVERT: J 184 GLU cc_start: 0.8854 (mm-30) cc_final: 0.8355 (mm-30) REVERT: J 193 GLU cc_start: 0.8653 (pm20) cc_final: 0.8368 (pm20) REVERT: J 227 LYS cc_start: 0.9468 (ttmm) cc_final: 0.9003 (tptp) REVERT: C 42 LEU cc_start: 0.9095 (mm) cc_final: 0.8721 (pp) REVERT: C 230 MET cc_start: 0.9121 (tmm) cc_final: 0.8527 (tmm) REVERT: C 248 TYR cc_start: 0.8761 (OUTLIER) cc_final: 0.8014 (m-80) REVERT: D 212 GLU cc_start: 0.8536 (tt0) cc_final: 0.8134 (tt0) REVERT: D 227 LYS cc_start: 0.9472 (ttmm) cc_final: 0.8989 (tttp) outliers start: 72 outliers final: 49 residues processed: 289 average time/residue: 0.3272 time to fit residues: 142.8486 Evaluate side-chains 293 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 235 time to evaluate : 2.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 75 LYS Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 205 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 137 optimal weight: 40.0000 chunk 88 optimal weight: 5.9990 chunk 132 optimal weight: 9.9990 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 140 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 109 optimal weight: 0.9990 chunk 20 optimal weight: 8.9990 chunk 174 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 173 GLN H 72 GLN E 100 ASN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 72 GLN D 231 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 19540 Z= 0.322 Angle : 0.646 13.067 26490 Z= 0.320 Chirality : 0.043 0.183 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.503 18.466 2530 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 3.38 % Allowed : 17.70 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.18), residues: 2310 helix: 1.25 (0.19), residues: 735 sheet: -0.55 (0.18), residues: 840 loop : -1.07 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 186 HIS 0.014 0.002 HIS A 119 PHE 0.011 0.001 PHE D 40 TYR 0.019 0.001 TYR G 202 ARG 0.004 0.000 ARG G 229 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 251 time to evaluate : 2.476 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 PHE cc_start: 0.8904 (OUTLIER) cc_final: 0.8693 (m-80) REVERT: A 100 ASN cc_start: 0.8455 (m-40) cc_final: 0.8248 (m110) REVERT: A 116 LYS cc_start: 0.8839 (mmmt) cc_final: 0.8548 (tptt) REVERT: A 248 TYR cc_start: 0.8794 (OUTLIER) cc_final: 0.8063 (m-80) REVERT: B 116 LYS cc_start: 0.8883 (mppt) cc_final: 0.8516 (mttp) REVERT: B 193 GLU cc_start: 0.8573 (pm20) cc_final: 0.8310 (pm20) REVERT: B 227 LYS cc_start: 0.9321 (ttmm) cc_final: 0.9083 (tptp) REVERT: G 172 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.8532 (tt0) REVERT: G 248 TYR cc_start: 0.8928 (OUTLIER) cc_final: 0.8084 (m-80) REVERT: H 130 TYR cc_start: 0.9150 (m-10) cc_final: 0.8815 (m-10) REVERT: H 184 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8242 (mm-30) REVERT: H 195 LYS cc_start: 0.8959 (mmmm) cc_final: 0.8695 (mmmm) REVERT: H 221 HIS cc_start: 0.8993 (OUTLIER) cc_final: 0.8704 (t-90) REVERT: H 227 LYS cc_start: 0.9425 (ttmm) cc_final: 0.8984 (tptp) REVERT: E 42 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8748 (pp) REVERT: E 88 ASP cc_start: 0.8603 (p0) cc_final: 0.8342 (p0) REVERT: E 202 TYR cc_start: 0.8727 (m-80) cc_final: 0.8376 (m-80) REVERT: E 248 TYR cc_start: 0.8797 (OUTLIER) cc_final: 0.8017 (m-80) REVERT: F 104 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8872 (mmmt) REVERT: F 194 ASP cc_start: 0.8361 (t0) cc_final: 0.8153 (m-30) REVERT: F 195 LYS cc_start: 0.9294 (mmmm) cc_final: 0.8914 (mmmm) REVERT: I 42 LEU cc_start: 0.9068 (mm) cc_final: 0.8735 (pp) REVERT: I 202 TYR cc_start: 0.8577 (m-80) cc_final: 0.8347 (m-80) REVERT: I 248 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8059 (m-80) REVERT: J 101 MET cc_start: 0.8848 (ppp) cc_final: 0.8478 (ppp) REVERT: J 184 GLU cc_start: 0.8837 (mm-30) cc_final: 0.8332 (mm-30) REVERT: J 193 GLU cc_start: 0.8628 (pm20) cc_final: 0.8293 (pm20) REVERT: J 227 LYS cc_start: 0.9484 (ttmm) cc_final: 0.9009 (tptp) REVERT: J 230 MET cc_start: 0.8622 (tmm) cc_final: 0.7821 (tmm) REVERT: C 42 LEU cc_start: 0.9080 (mm) cc_final: 0.8704 (pp) REVERT: C 202 TYR cc_start: 0.8862 (m-80) cc_final: 0.8643 (m-80) REVERT: C 230 MET cc_start: 0.9068 (tmm) cc_final: 0.8437 (tmm) REVERT: C 248 TYR cc_start: 0.8758 (OUTLIER) cc_final: 0.8001 (m-80) REVERT: D 212 GLU cc_start: 0.8466 (tt0) cc_final: 0.8058 (tt0) REVERT: D 227 LYS cc_start: 0.9470 (ttmm) cc_final: 0.9010 (tttp) outliers start: 75 outliers final: 51 residues processed: 292 average time/residue: 0.3184 time to fit residues: 141.9951 Evaluate side-chains 296 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 235 time to evaluate : 2.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 97 MET Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 221 HIS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 20 VAL Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 68 THR Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 172 GLU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 165 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 201 optimal weight: 8.9990 chunk 212 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 chunk 124 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 162 optimal weight: 30.0000 chunk 63 optimal weight: 2.9990 chunk 186 optimal weight: 20.0000 chunk 195 optimal weight: 5.9990 chunk 205 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 100 ASN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.4019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19540 Z= 0.326 Angle : 0.668 16.176 26490 Z= 0.327 Chirality : 0.043 0.185 3110 Planarity : 0.004 0.037 3340 Dihedral : 4.506 19.408 2530 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.33 % Allowed : 17.97 % Favored : 78.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.18), residues: 2310 helix: 1.27 (0.19), residues: 735 sheet: -0.52 (0.18), residues: 850 loop : -1.03 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP H 186 HIS 0.015 0.002 HIS A 119 PHE 0.010 0.001 PHE D 40 TYR 0.013 0.001 TYR D 103 ARG 0.004 0.000 ARG G 229 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 236 time to evaluate : 2.310 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 88 ASP cc_start: 0.8786 (p0) cc_final: 0.8531 (p0) REVERT: A 100 ASN cc_start: 0.8491 (m-40) cc_final: 0.8060 (m-40) REVERT: A 116 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8592 (tptt) REVERT: A 248 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8160 (m-80) REVERT: B 116 LYS cc_start: 0.8864 (mppt) cc_final: 0.8484 (mttp) REVERT: B 227 LYS cc_start: 0.9315 (ttmm) cc_final: 0.8894 (tptp) REVERT: G 172 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8514 (tt0) REVERT: G 202 TYR cc_start: 0.8548 (m-80) cc_final: 0.8326 (m-80) REVERT: G 248 TYR cc_start: 0.8957 (OUTLIER) cc_final: 0.8164 (m-80) REVERT: H 130 TYR cc_start: 0.9155 (m-10) cc_final: 0.8813 (m-10) REVERT: H 184 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8258 (mm-30) REVERT: H 221 HIS cc_start: 0.8999 (OUTLIER) cc_final: 0.8736 (t-90) REVERT: H 227 LYS cc_start: 0.9419 (ttmm) cc_final: 0.8956 (tptp) REVERT: E 42 LEU cc_start: 0.9100 (OUTLIER) cc_final: 0.8770 (pp) REVERT: E 88 ASP cc_start: 0.8595 (p0) cc_final: 0.8327 (p0) REVERT: E 248 TYR cc_start: 0.8799 (OUTLIER) cc_final: 0.8013 (m-80) REVERT: F 104 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8866 (mmmt) REVERT: F 194 ASP cc_start: 0.8369 (t0) cc_final: 0.8166 (m-30) REVERT: F 195 LYS cc_start: 0.9296 (mmmm) cc_final: 0.8930 (mmmm) REVERT: I 42 LEU cc_start: 0.9084 (mm) cc_final: 0.8765 (pp) REVERT: I 166 MET cc_start: 0.8672 (mmt) cc_final: 0.8291 (mmp) REVERT: I 202 TYR cc_start: 0.8573 (m-80) cc_final: 0.8352 (m-80) REVERT: I 248 TYR cc_start: 0.8846 (OUTLIER) cc_final: 0.8066 (m-80) REVERT: J 184 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8341 (mm-30) REVERT: J 193 GLU cc_start: 0.8569 (pm20) cc_final: 0.8196 (pm20) REVERT: J 221 HIS cc_start: 0.8973 (OUTLIER) cc_final: 0.8744 (t-90) REVERT: J 227 LYS cc_start: 0.9473 (ttmm) cc_final: 0.8982 (tptp) REVERT: J 230 MET cc_start: 0.8667 (tmm) cc_final: 0.7666 (tmm) REVERT: C 42 LEU cc_start: 0.9096 (mm) cc_final: 0.8726 (pp) REVERT: C 230 MET cc_start: 0.8912 (tmm) cc_final: 0.8331 (tmm) REVERT: C 248 TYR cc_start: 0.8788 (OUTLIER) cc_final: 0.8018 (m-80) REVERT: D 227 LYS cc_start: 0.9458 (ttmm) cc_final: 0.9009 (tttp) outliers start: 74 outliers final: 53 residues processed: 275 average time/residue: 0.3309 time to fit residues: 137.6037 Evaluate side-chains 294 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 231 time to evaluate : 2.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 68 THR Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 166 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 248 TYR Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 221 HIS Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 75 LYS Chi-restraints excluded: chain G residue 97 MET Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 172 GLU Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain H residue 221 HIS Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 243 LYS Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 189 THR Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 97 MET Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 117 THR Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 68 THR Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain J residue 221 HIS Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 166 MET Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 97 MET Chi-restraints excluded: chain D residue 165 SER Chi-restraints excluded: chain D residue 205 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 135 optimal weight: 9.9990 chunk 218 optimal weight: 7.9990 chunk 133 optimal weight: 0.2980 chunk 103 optimal weight: 1.9990 chunk 151 optimal weight: 4.9990 chunk 229 optimal weight: 8.9990 chunk 210 optimal weight: 0.3980 chunk 182 optimal weight: 8.9990 chunk 18 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 GLN ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19540 Z= 0.201 Angle : 0.644 13.943 26490 Z= 0.314 Chirality : 0.044 0.183 3110 Planarity : 0.004 0.038 3340 Dihedral : 4.329 20.147 2530 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.39 % Allowed : 18.96 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.18), residues: 2310 helix: 1.34 (0.19), residues: 735 sheet: -0.40 (0.18), residues: 830 loop : -0.82 (0.24), residues: 745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 186 HIS 0.015 0.002 HIS A 119 PHE 0.014 0.001 PHE A 255 TYR 0.017 0.001 TYR A 41 ARG 0.003 0.000 ARG C 229 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4620 Ramachandran restraints generated. 2310 Oldfield, 0 Emsley, 2310 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 274 time to evaluate : 2.334 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: A 37 TYR cc_start: 0.8979 (t80) cc_final: 0.8632 (m-80) REVERT: A 100 ASN cc_start: 0.8502 (m-40) cc_final: 0.8078 (m-40) REVERT: B 116 LYS cc_start: 0.8869 (mppt) cc_final: 0.8502 (mttp) REVERT: G 42 LEU cc_start: 0.9013 (mm) cc_final: 0.8639 (pp) REVERT: G 202 TYR cc_start: 0.8488 (m-80) cc_final: 0.8209 (m-80) REVERT: G 248 TYR cc_start: 0.8946 (OUTLIER) cc_final: 0.8071 (m-80) REVERT: H 130 TYR cc_start: 0.9122 (m-10) cc_final: 0.8792 (m-10) REVERT: H 227 LYS cc_start: 0.9422 (ttmm) cc_final: 0.9034 (tptp) REVERT: E 42 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8766 (pp) REVERT: E 88 ASP cc_start: 0.8549 (p0) cc_final: 0.8251 (p0) REVERT: E 202 TYR cc_start: 0.8605 (m-80) cc_final: 0.8273 (m-80) REVERT: E 248 TYR cc_start: 0.8825 (OUTLIER) cc_final: 0.8096 (m-80) REVERT: F 17 TYR cc_start: 0.6141 (p90) cc_final: 0.5587 (p90) REVERT: F 104 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8895 (mmmt) REVERT: F 195 LYS cc_start: 0.9249 (mmmm) cc_final: 0.8819 (mmmm) REVERT: I 42 LEU cc_start: 0.9060 (mm) cc_final: 0.8765 (pp) REVERT: I 116 LYS cc_start: 0.8276 (tptt) cc_final: 0.7924 (mmmt) REVERT: I 202 TYR cc_start: 0.8486 (m-80) cc_final: 0.8276 (m-80) REVERT: I 248 TYR cc_start: 0.8847 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: J 184 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8277 (mm-30) REVERT: J 193 GLU cc_start: 0.8556 (pm20) cc_final: 0.8188 (pm20) REVERT: J 227 LYS cc_start: 0.9455 (ttmm) cc_final: 0.9049 (tptp) REVERT: C 42 LEU cc_start: 0.9078 (mm) cc_final: 0.8704 (pp) REVERT: C 101 MET cc_start: 0.8620 (tpp) cc_final: 0.8372 (tpp) REVERT: C 248 TYR cc_start: 0.8835 (OUTLIER) cc_final: 0.8177 (m-80) REVERT: D 212 GLU cc_start: 0.8460 (tt0) cc_final: 0.8055 (tt0) REVERT: D 227 LYS cc_start: 0.9462 (ttmm) cc_final: 0.9023 (tttp) outliers start: 53 outliers final: 37 residues processed: 304 average time/residue: 0.3201 time to fit residues: 148.0600 Evaluate side-chains 281 residues out of total 2220 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 238 time to evaluate : 2.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain A residue 97 MET Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain A residue 257 CYS Chi-restraints excluded: chain B residue 25 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain G residue 109 LEU Chi-restraints excluded: chain G residue 248 TYR Chi-restraints excluded: chain G residue 257 CYS Chi-restraints excluded: chain H residue 68 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain E residue 42 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 172 GLU Chi-restraints excluded: chain E residue 239 LEU Chi-restraints excluded: chain E residue 248 TYR Chi-restraints excluded: chain E residue 257 CYS Chi-restraints excluded: chain F residue 25 GLN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 75 LYS Chi-restraints excluded: chain F residue 104 LYS Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain I residue 40 PHE Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 189 THR Chi-restraints excluded: chain I residue 248 TYR Chi-restraints excluded: chain I residue 257 CYS Chi-restraints excluded: chain J residue 20 VAL Chi-restraints excluded: chain J residue 25 GLN Chi-restraints excluded: chain J residue 189 THR Chi-restraints excluded: chain J residue 205 ILE Chi-restraints excluded: chain C residue 40 PHE Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 248 TYR Chi-restraints excluded: chain C residue 257 CYS Chi-restraints excluded: chain D residue 20 VAL Chi-restraints excluded: chain D residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 230 random chunks: chunk 144 optimal weight: 6.9990 chunk 194 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 168 optimal weight: 0.0870 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 76 optimal weight: 0.5980 chunk 187 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.8562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 ASN ** B 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 169 GLN E 100 ASN I 38 HIS ** J 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.080287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.053078 restraints weight = 71642.835| |-----------------------------------------------------------------------------| r_work (start): 0.2860 rms_B_bonded: 4.71 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.4287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19540 Z= 0.199 Angle : 0.660 13.728 26490 Z= 0.323 Chirality : 0.044 0.181 3110 Planarity : 0.004 0.039 3340 Dihedral : 4.332 21.994 2530 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.71 % Allowed : 20.27 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.18), residues: 2310 helix: 1.43 (0.19), residues: 730 sheet: -0.36 (0.18), residues: 830 loop : -0.77 (0.25), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 186 HIS 0.025 0.002 HIS A 119 PHE 0.012 0.001 PHE A 255 TYR 0.039 0.002 TYR I 41 ARG 0.006 0.000 ARG E 98 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3737.63 seconds wall clock time: 70 minutes 15.29 seconds (4215.29 seconds total)