Starting phenix.real_space_refine on Fri Sep 27 18:22:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/09_2024/6lqj_0947.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/09_2024/6lqj_0947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/09_2024/6lqj_0947.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/09_2024/6lqj_0947.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/09_2024/6lqj_0947.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lqj_0947/09_2024/6lqj_0947.cif" } resolution = 3.24 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= 0.005 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 54 5.16 5 C 10791 2.51 5 N 2925 2.21 5 O 3330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 126 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 17100 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1589 Classifications: {'peptide': 206} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 199} Chain: "a" Number of atoms: 311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 311 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Restraints were copied for chains: C, B, E, D, G, F, I, H, f, c, g, b, h, e, i, d Time building chain proxies: 5.18, per 1000 atoms: 0.30 Number of scatterers: 17100 At special positions: 0 Unit cell: (111, 112, 123, 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 54 16.00 O 3330 8.00 N 2925 7.00 C 10791 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: 4.47 Conformation dependent library (CDL) restraints added in 2.2 seconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4032 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 18 sheets defined 26.0% alpha, 40.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 81 through 90 Processing helix chain 'A' and resid 100 through 115 Processing helix chain 'A' and resid 226 through 249 Processing helix chain 'B' and resid 81 through 90 Processing helix chain 'B' and resid 100 through 115 Processing helix chain 'B' and resid 226 through 249 Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 100 through 115 Processing helix chain 'C' and resid 226 through 249 Processing helix chain 'D' and resid 81 through 90 Processing helix chain 'D' and resid 100 through 115 Processing helix chain 'D' and resid 226 through 249 Processing helix chain 'E' and resid 81 through 90 Processing helix chain 'E' and resid 100 through 115 Processing helix chain 'E' and resid 226 through 249 Processing helix chain 'F' and resid 81 through 90 Processing helix chain 'F' and resid 100 through 115 Processing helix chain 'F' and resid 226 through 249 Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 100 through 115 Processing helix chain 'G' and resid 226 through 249 Processing helix chain 'H' and resid 81 through 90 Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 226 through 249 Processing helix chain 'I' and resid 81 through 90 Processing helix chain 'I' and resid 100 through 115 Processing helix chain 'I' and resid 226 through 249 Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 37 through 47 Processing helix chain 'b' and resid 34 through 36 No H-bonds generated for 'chain 'b' and resid 34 through 36' Processing helix chain 'b' and resid 37 through 47 Processing helix chain 'c' and resid 34 through 36 No H-bonds generated for 'chain 'c' and resid 34 through 36' Processing helix chain 'c' and resid 37 through 47 Processing helix chain 'd' and resid 34 through 36 No H-bonds generated for 'chain 'd' and resid 34 through 36' Processing helix chain 'd' and resid 37 through 47 Processing helix chain 'e' and resid 34 through 36 No H-bonds generated for 'chain 'e' and resid 34 through 36' Processing helix chain 'e' and resid 37 through 47 Processing helix chain 'f' and resid 34 through 36 No H-bonds generated for 'chain 'f' and resid 34 through 36' Processing helix chain 'f' and resid 37 through 47 Processing helix chain 'g' and resid 34 through 36 No H-bonds generated for 'chain 'g' and resid 34 through 36' Processing helix chain 'g' and resid 37 through 47 Processing helix chain 'h' and resid 34 through 36 No H-bonds generated for 'chain 'h' and resid 34 through 36' Processing helix chain 'h' and resid 37 through 47 Processing helix chain 'i' and resid 34 through 36 No H-bonds generated for 'chain 'i' and resid 34 through 36' Processing helix chain 'i' and resid 37 through 47 Processing sheet with id=AA1, first strand: chain 'A' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE A 49 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU A 96 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 51 " --> pdb=" O LEU A 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.254A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU A 139 " --> pdb=" O VAL A 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL A 179 " --> pdb=" O GLU A 139 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER A 141 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG A 177 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE A 143 " --> pdb=" O ASN A 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN A 175 " --> pdb=" O ILE A 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR A 145 " --> pdb=" O ALA A 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA A 173 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER A 147 " --> pdb=" O GLN A 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN A 171 " --> pdb=" O SER A 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU A 169 " --> pdb=" O VAL A 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER A 151 " --> pdb=" O TYR A 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR A 167 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY A 153 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 165 " --> pdb=" O GLY A 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY A 155 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 163 " --> pdb=" O GLY A 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN A 180 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE A 186 " --> pdb=" O ASN A 180 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ARG A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N VAL I 149 " --> pdb=" O ASN A 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN I 57 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY I 144 " --> pdb=" O GLN I 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU I 139 " --> pdb=" O VAL I 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL I 179 " --> pdb=" O GLU I 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER I 141 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG I 177 " --> pdb=" O SER I 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE I 143 " --> pdb=" O ASN I 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN I 175 " --> pdb=" O ILE I 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR I 145 " --> pdb=" O ALA I 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA I 173 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER I 147 " --> pdb=" O GLN I 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN I 171 " --> pdb=" O SER I 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU I 169 " --> pdb=" O VAL I 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER I 151 " --> pdb=" O TYR I 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR I 167 " --> pdb=" O SER I 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY I 153 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR I 165 " --> pdb=" O GLY I 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY I 155 " --> pdb=" O ALA I 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA I 163 " --> pdb=" O GLY I 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN I 180 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE I 186 " --> pdb=" O ASN I 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG I 213 " --> pdb=" O ILE I 209 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL G 149 " --> pdb=" O ASN I 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN G 57 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY G 144 " --> pdb=" O GLN G 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU G 139 " --> pdb=" O VAL G 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL G 179 " --> pdb=" O GLU G 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER G 141 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG G 177 " --> pdb=" O SER G 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE G 143 " --> pdb=" O ASN G 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN G 175 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR G 145 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA G 173 " --> pdb=" O TYR G 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER G 147 " --> pdb=" O GLN G 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN G 171 " --> pdb=" O SER G 147 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LEU G 169 " --> pdb=" O VAL G 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER G 151 " --> pdb=" O TYR G 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR G 167 " --> pdb=" O SER G 151 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N GLY G 153 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR G 165 " --> pdb=" O GLY G 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY G 155 " --> pdb=" O ALA G 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA G 163 " --> pdb=" O GLY G 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN G 180 " --> pdb=" O ILE G 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE G 186 " --> pdb=" O ASN G 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG G 213 " --> pdb=" O ILE G 209 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL C 149 " --> pdb=" O ASN G 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN C 57 " --> pdb=" O ILE C 142 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N GLY C 144 " --> pdb=" O GLN C 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU C 139 " --> pdb=" O VAL C 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL C 179 " --> pdb=" O GLU C 139 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N SER C 141 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG C 177 " --> pdb=" O SER C 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE C 143 " --> pdb=" O ASN C 175 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASN C 175 " --> pdb=" O ILE C 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR C 145 " --> pdb=" O ALA C 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA C 173 " --> pdb=" O TYR C 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER C 147 " --> pdb=" O GLN C 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN C 171 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU C 169 " --> pdb=" O VAL C 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER C 151 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR C 167 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY C 153 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR C 165 " --> pdb=" O GLY C 153 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N GLY C 155 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA C 163 " --> pdb=" O GLY C 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN C 180 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE C 186 " --> pdb=" O ASN C 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N VAL D 149 " --> pdb=" O ASN C 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN D 57 " --> pdb=" O ILE D 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY D 144 " --> pdb=" O GLN D 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU D 139 " --> pdb=" O VAL D 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL D 179 " --> pdb=" O GLU D 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER D 141 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ARG D 177 " --> pdb=" O SER D 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE D 143 " --> pdb=" O ASN D 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN D 175 " --> pdb=" O ILE D 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR D 145 " --> pdb=" O ALA D 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA D 173 " --> pdb=" O TYR D 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER D 147 " --> pdb=" O GLN D 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN D 171 " --> pdb=" O SER D 147 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU D 169 " --> pdb=" O VAL D 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER D 151 " --> pdb=" O TYR D 167 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR D 167 " --> pdb=" O SER D 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY D 153 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR D 165 " --> pdb=" O GLY D 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY D 155 " --> pdb=" O ALA D 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA D 163 " --> pdb=" O GLY D 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN D 180 " --> pdb=" O ILE D 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE D 186 " --> pdb=" O ASN D 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N VAL F 149 " --> pdb=" O ASN D 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN F 57 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N GLY F 144 " --> pdb=" O GLN F 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU F 139 " --> pdb=" O VAL F 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL F 179 " --> pdb=" O GLU F 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER F 141 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG F 177 " --> pdb=" O SER F 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE F 143 " --> pdb=" O ASN F 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN F 175 " --> pdb=" O ILE F 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR F 145 " --> pdb=" O ALA F 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA F 173 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER F 147 " --> pdb=" O GLN F 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN F 171 " --> pdb=" O SER F 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU F 169 " --> pdb=" O VAL F 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER F 151 " --> pdb=" O TYR F 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR F 167 " --> pdb=" O SER F 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY F 153 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR F 165 " --> pdb=" O GLY F 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY F 155 " --> pdb=" O ALA F 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA F 163 " --> pdb=" O GLY F 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN F 180 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE F 186 " --> pdb=" O ASN F 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG F 213 " --> pdb=" O ILE F 209 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N VAL H 149 " --> pdb=" O ASN F 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN H 57 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY H 144 " --> pdb=" O GLN H 57 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 56 through 57 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 56 through 57 current: chain 'H' and resid 162 through 180 removed outlier: 6.269A pdb=" N ASN H 180 " --> pdb=" O ILE H 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE H 186 " --> pdb=" O ASN H 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG H 213 " --> pdb=" O ILE H 209 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL E 149 " --> pdb=" O ASN H 224 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 56 through 57 removed outlier: 7.254A pdb=" N GLN E 57 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY E 144 " --> pdb=" O GLN E 57 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLU E 139 " --> pdb=" O VAL E 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N VAL E 179 " --> pdb=" O GLU E 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER E 141 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG E 177 " --> pdb=" O SER E 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE E 143 " --> pdb=" O ASN E 175 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N ASN E 175 " --> pdb=" O ILE E 143 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N TYR E 145 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N ALA E 173 " --> pdb=" O TYR E 145 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N SER E 147 " --> pdb=" O GLN E 171 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLN E 171 " --> pdb=" O SER E 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU E 169 " --> pdb=" O VAL E 149 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N SER E 151 " --> pdb=" O TYR E 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR E 167 " --> pdb=" O SER E 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY E 153 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR E 165 " --> pdb=" O GLY E 153 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N GLY E 155 " --> pdb=" O ALA E 163 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA E 163 " --> pdb=" O GLY E 155 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ASN E 180 " --> pdb=" O ILE E 186 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N ILE E 186 " --> pdb=" O ASN E 180 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG E 213 " --> pdb=" O ILE E 209 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N VAL B 149 " --> pdb=" O ASN E 224 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.253A pdb=" N GLN B 57 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY B 144 " --> pdb=" O GLN B 57 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLU B 139 " --> pdb=" O VAL B 179 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL B 179 " --> pdb=" O GLU B 139 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N SER B 141 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ARG B 177 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ILE B 143 " --> pdb=" O ASN B 175 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N ASN B 175 " --> pdb=" O ILE B 143 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N TYR B 145 " --> pdb=" O ALA B 173 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N ALA B 173 " --> pdb=" O TYR B 145 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N SER B 147 " --> pdb=" O GLN B 171 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN B 171 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU B 169 " --> pdb=" O VAL B 149 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N SER B 151 " --> pdb=" O TYR B 167 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TYR B 167 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLY B 153 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N THR B 165 " --> pdb=" O GLY B 153 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N GLY B 155 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA B 163 " --> pdb=" O GLY B 155 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN B 180 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ILE B 186 " --> pdb=" O ASN B 180 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N VAL A 149 " --> pdb=" O ASN B 224 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N GLN A 57 " --> pdb=" O ILE A 142 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N GLY A 144 " --> pdb=" O GLN A 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE B 49 " --> pdb=" O ILE B 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU B 96 " --> pdb=" O ILE B 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 51 " --> pdb=" O LEU B 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE C 49 " --> pdb=" O ILE C 94 " (cutoff:3.500A) removed outlier: 7.118A pdb=" N LEU C 96 " --> pdb=" O ILE C 49 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL C 51 " --> pdb=" O LEU C 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE D 49 " --> pdb=" O ILE D 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU D 96 " --> pdb=" O ILE D 49 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL D 51 " --> pdb=" O LEU D 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE E 49 " --> pdb=" O ILE E 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU E 96 " --> pdb=" O ILE E 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL E 51 " --> pdb=" O LEU E 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'F' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE F 49 " --> pdb=" O ILE F 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU F 96 " --> pdb=" O ILE F 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL F 51 " --> pdb=" O LEU F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'G' and resid 49 through 52 removed outlier: 6.110A pdb=" N ILE G 49 " --> pdb=" O ILE G 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU G 96 " --> pdb=" O ILE G 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL G 51 " --> pdb=" O LEU G 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'H' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE H 49 " --> pdb=" O ILE H 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU H 96 " --> pdb=" O ILE H 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL H 51 " --> pdb=" O LEU H 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'I' and resid 49 through 52 removed outlier: 6.111A pdb=" N ILE I 49 " --> pdb=" O ILE I 94 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N LEU I 96 " --> pdb=" O ILE I 49 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL I 51 " --> pdb=" O LEU I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 755 hydrogen bonds defined for protein. 2238 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.40 Time building geometry restraints manager: 5.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5751 1.34 - 1.45: 2233 1.45 - 1.57: 9314 1.57 - 1.68: 0 1.68 - 1.80: 99 Bond restraints: 17397 Sorted by residual: bond pdb=" CA ASP B 164 " pdb=" CB ASP B 164 " ideal model delta sigma weight residual 1.534 1.512 0.023 1.77e-02 3.19e+03 1.65e+00 bond pdb=" CG PRO D 67 " pdb=" CD PRO D 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.59e+00 bond pdb=" CA ASP H 164 " pdb=" CB ASP H 164 " ideal model delta sigma weight residual 1.534 1.512 0.022 1.77e-02 3.19e+03 1.58e+00 bond pdb=" CG PRO A 67 " pdb=" CD PRO A 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.57e+00 bond pdb=" CG PRO E 67 " pdb=" CD PRO E 67 " ideal model delta sigma weight residual 1.512 1.478 0.034 2.70e-02 1.37e+03 1.55e+00 ... (remaining 17392 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 22055 1.35 - 2.70: 1271 2.70 - 4.05: 227 4.05 - 5.40: 36 5.40 - 6.75: 9 Bond angle restraints: 23598 Sorted by residual: angle pdb=" CA PHE f 31 " pdb=" CB PHE f 31 " pdb=" CG PHE f 31 " ideal model delta sigma weight residual 113.80 116.91 -3.11 1.00e+00 1.00e+00 9.66e+00 angle pdb=" CA PHE i 31 " pdb=" CB PHE i 31 " pdb=" CG PHE i 31 " ideal model delta sigma weight residual 113.80 116.90 -3.10 1.00e+00 1.00e+00 9.58e+00 angle pdb=" CA PHE a 31 " pdb=" CB PHE a 31 " pdb=" CG PHE a 31 " ideal model delta sigma weight residual 113.80 116.88 -3.08 1.00e+00 1.00e+00 9.51e+00 angle pdb=" CA PHE d 31 " pdb=" CB PHE d 31 " pdb=" CG PHE d 31 " ideal model delta sigma weight residual 113.80 116.88 -3.08 1.00e+00 1.00e+00 9.49e+00 angle pdb=" CA PHE e 31 " pdb=" CB PHE e 31 " pdb=" CG PHE e 31 " ideal model delta sigma weight residual 113.80 116.86 -3.06 1.00e+00 1.00e+00 9.35e+00 ... (remaining 23593 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 8896 15.66 - 31.31: 1010 31.31 - 46.97: 291 46.97 - 62.62: 135 62.62 - 78.28: 18 Dihedral angle restraints: 10350 sinusoidal: 4032 harmonic: 6318 Sorted by residual: dihedral pdb=" CA GLY f 32 " pdb=" C GLY f 32 " pdb=" N GLY f 33 " pdb=" CA GLY f 33 " ideal model delta harmonic sigma weight residual 180.00 148.98 31.02 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY d 32 " pdb=" C GLY d 32 " pdb=" N GLY d 33 " pdb=" CA GLY d 33 " ideal model delta harmonic sigma weight residual 180.00 148.98 31.02 0 5.00e+00 4.00e-02 3.85e+01 dihedral pdb=" CA GLY e 32 " pdb=" C GLY e 32 " pdb=" N GLY e 33 " pdb=" CA GLY e 33 " ideal model delta harmonic sigma weight residual 180.00 149.02 30.98 0 5.00e+00 4.00e-02 3.84e+01 ... (remaining 10347 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 1530 0.036 - 0.072: 831 0.072 - 0.108: 179 0.108 - 0.145: 102 0.145 - 0.181: 13 Chirality restraints: 2655 Sorted by residual: chirality pdb=" CA PHE h 31 " pdb=" N PHE h 31 " pdb=" C PHE h 31 " pdb=" CB PHE h 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.16e-01 chirality pdb=" CA PHE i 31 " pdb=" N PHE i 31 " pdb=" C PHE i 31 " pdb=" CB PHE i 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 chirality pdb=" CA PHE e 31 " pdb=" N PHE e 31 " pdb=" C PHE e 31 " pdb=" CB PHE e 31 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.06e-01 ... (remaining 2652 not shown) Planarity restraints: 3123 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE g 31 " -0.019 2.00e-02 2.50e+03 1.74e-02 5.29e+00 pdb=" CG PHE g 31 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE g 31 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE g 31 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE g 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE g 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE g 31 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE e 31 " 0.019 2.00e-02 2.50e+03 1.73e-02 5.27e+00 pdb=" CG PHE e 31 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE e 31 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE e 31 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE e 31 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE e 31 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE e 31 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE c 31 " -0.019 2.00e-02 2.50e+03 1.73e-02 5.25e+00 pdb=" CG PHE c 31 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 PHE c 31 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE c 31 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE c 31 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE c 31 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE c 31 " -0.003 2.00e-02 2.50e+03 ... (remaining 3120 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 2731 2.75 - 3.29: 16427 3.29 - 3.83: 29104 3.83 - 4.36: 35687 4.36 - 4.90: 64804 Nonbonded interactions: 148753 Sorted by model distance: nonbonded pdb=" OD1 ASN I 224 " pdb=" N MET i 22 " model vdw 2.216 3.120 nonbonded pdb=" O GLN A 102 " pdb=" ND2 ASN A 106 " model vdw 2.226 3.120 nonbonded pdb=" O GLN H 102 " pdb=" ND2 ASN H 106 " model vdw 2.226 3.120 nonbonded pdb=" O GLN G 102 " pdb=" ND2 ASN G 106 " model vdw 2.227 3.120 nonbonded pdb=" O GLN I 102 " pdb=" ND2 ASN I 106 " model vdw 2.227 3.120 ... (remaining 148748 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' } 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' } 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: 0.710 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: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.170 Process input model: 31.940 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.060 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: 0.000 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 0.044 17397 Z= 0.456 Angle : 0.739 6.750 23598 Z= 0.435 Chirality : 0.048 0.181 2655 Planarity : 0.004 0.039 3123 Dihedral : 16.291 78.277 6318 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.34 % Allowed : 15.53 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.16), residues: 2178 helix: -1.56 (0.17), residues: 603 sheet: -1.31 (0.21), residues: 693 loop : -3.29 (0.17), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 252 PHE 0.040 0.003 PHE g 31 TYR 0.015 0.001 TYR B 158 ARG 0.003 0.001 ARG b 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 287 time to evaluate : 1.898 Fit side-chains REVERT: A 215 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8302 (tp) REVERT: C 59 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7923 (mt-10) REVERT: C 137 MET cc_start: 0.8214 (ttm) cc_final: 0.7706 (ttm) REVERT: C 139 GLU cc_start: 0.7567 (mm-30) cc_final: 0.7328 (mm-30) REVERT: C 213 ARG cc_start: 0.8682 (mmt-90) cc_final: 0.8279 (mpt180) REVERT: C 228 MET cc_start: 0.8442 (ptt) cc_final: 0.8100 (ptp) REVERT: D 75 VAL cc_start: 0.9147 (t) cc_final: 0.8878 (m) REVERT: D 107 GLU cc_start: 0.8490 (tp30) cc_final: 0.8243 (tp30) REVERT: D 131 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7891 (mp) REVERT: D 139 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7211 (mm-30) REVERT: F 59 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8069 (mt-10) REVERT: F 75 VAL cc_start: 0.9158 (t) cc_final: 0.8890 (m) REVERT: F 139 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7111 (mm-30) REVERT: F 240 ILE cc_start: 0.8747 (mm) cc_final: 0.8500 (mm) REVERT: G 59 GLU cc_start: 0.8270 (mt-10) cc_final: 0.8058 (mt-10) REVERT: G 75 VAL cc_start: 0.9142 (t) cc_final: 0.8890 (m) REVERT: G 137 MET cc_start: 0.8192 (ttm) cc_final: 0.7933 (ttp) REVERT: G 207 ARG cc_start: 0.7469 (ptt90) cc_final: 0.7266 (ptm-80) REVERT: G 213 ARG cc_start: 0.8586 (mmt-90) cc_final: 0.8328 (mpt180) REVERT: H 75 VAL cc_start: 0.9101 (t) cc_final: 0.8841 (m) REVERT: H 213 ARG cc_start: 0.8620 (mmt-90) cc_final: 0.8255 (mmt180) REVERT: I 170 ASP cc_start: 0.8151 (m-30) cc_final: 0.7898 (m-30) REVERT: I 213 ARG cc_start: 0.8552 (mmt-90) cc_final: 0.8195 (mpt180) REVERT: I 215 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.8165 (tt) REVERT: a 22 MET cc_start: 0.8715 (mtt) cc_final: 0.8450 (mtt) REVERT: a 52 LYS cc_start: 0.8528 (mppt) cc_final: 0.8100 (mppt) REVERT: e 22 MET cc_start: 0.8679 (mtt) cc_final: 0.8425 (mtt) REVERT: e 52 LYS cc_start: 0.8508 (mppt) cc_final: 0.8304 (mtmm) REVERT: f 52 LYS cc_start: 0.8402 (mppt) cc_final: 0.8165 (mtmm) REVERT: i 22 MET cc_start: 0.8843 (mtt) cc_final: 0.8569 (mtp) outliers start: 99 outliers final: 51 residues processed: 371 average time/residue: 0.3074 time to fit residues: 166.9405 Evaluate side-chains 306 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 252 time to evaluate : 1.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 237 THR Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 192 THR Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 198 SER Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 237 THR Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 198 SER Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 198 SER Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 198 SER Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 237 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 163 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 169 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 3.9990 chunk 126 optimal weight: 0.9980 chunk 196 optimal weight: 1.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 62 GLN A 77 GLN A 148 ASN A 244 ASN B 77 GLN B 148 ASN B 244 ASN C 62 GLN C 77 GLN C 106 ASN C 148 ASN C 244 ASN D 62 GLN D 77 GLN D 106 ASN D 135 ASN D 148 ASN D 244 ASN E 62 GLN E 77 GLN E 106 ASN E 148 ASN E 244 ASN F 62 GLN F 77 GLN F 106 ASN F 148 ASN F 244 ASN G 62 GLN G 70 ASN G 77 GLN G 106 ASN ** G 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 244 ASN H 62 GLN H 77 GLN H 106 ASN H 148 ASN H 244 ASN I 77 GLN I 106 ASN I 148 ASN I 244 ASN a 28 ASN b 28 ASN b 36 ASN c 28 ASN d 28 ASN e 28 ASN f 28 ASN g 28 ASN h 28 ASN i 28 ASN Total number of N/Q/H flips: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17397 Z= 0.267 Angle : 0.602 8.713 23598 Z= 0.326 Chirality : 0.045 0.150 2655 Planarity : 0.004 0.041 3123 Dihedral : 8.432 57.153 2467 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.15 % Allowed : 16.94 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.23 (0.18), residues: 2178 helix: -0.08 (0.20), residues: 603 sheet: -1.04 (0.22), residues: 693 loop : -2.84 (0.18), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 252 PHE 0.027 0.002 PHE h 31 TYR 0.012 0.001 TYR E 158 ARG 0.002 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 266 time to evaluate : 1.885 Fit side-chains REVERT: A 137 MET cc_start: 0.7964 (OUTLIER) cc_final: 0.7547 (ttm) REVERT: B 131 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7762 (mp) REVERT: B 218 GLU cc_start: 0.7359 (pt0) cc_final: 0.7138 (pt0) REVERT: C 59 GLU cc_start: 0.8251 (mt-10) cc_final: 0.7883 (mt-10) REVERT: C 137 MET cc_start: 0.8108 (ttm) cc_final: 0.7625 (ttm) REVERT: C 139 GLU cc_start: 0.7495 (mm-30) cc_final: 0.7235 (mm-30) REVERT: C 218 GLU cc_start: 0.7427 (pt0) cc_final: 0.7226 (pt0) REVERT: D 59 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7886 (mt-10) REVERT: D 131 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7795 (mp) REVERT: D 139 GLU cc_start: 0.7420 (mm-30) cc_final: 0.7100 (mm-30) REVERT: F 59 GLU cc_start: 0.8243 (mt-10) cc_final: 0.7905 (mt-10) REVERT: F 139 GLU cc_start: 0.7355 (mm-30) cc_final: 0.7085 (mm-30) REVERT: F 225 GLU cc_start: 0.8390 (tt0) cc_final: 0.8105 (tt0) REVERT: F 240 ILE cc_start: 0.8818 (mm) cc_final: 0.8580 (mm) REVERT: G 131 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7822 (mp) REVERT: G 139 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7144 (mm-30) REVERT: G 240 ILE cc_start: 0.8792 (mm) cc_final: 0.8589 (mt) REVERT: H 59 GLU cc_start: 0.8153 (mt-10) cc_final: 0.7832 (mt-10) REVERT: H 131 LEU cc_start: 0.8231 (OUTLIER) cc_final: 0.7883 (mp) REVERT: H 137 MET cc_start: 0.8050 (OUTLIER) cc_final: 0.7553 (ttm) REVERT: H 139 GLU cc_start: 0.7449 (mm-30) cc_final: 0.7209 (mm-30) REVERT: H 213 ARG cc_start: 0.8644 (mmt-90) cc_final: 0.8431 (mpt180) REVERT: H 215 LEU cc_start: 0.8561 (OUTLIER) cc_final: 0.8314 (tp) REVERT: I 109 LYS cc_start: 0.9099 (mtpt) cc_final: 0.8842 (mtmt) REVERT: I 131 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7823 (mp) REVERT: I 213 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.8327 (mpt180) REVERT: I 232 MET cc_start: 0.8693 (tpt) cc_final: 0.7870 (tpt) REVERT: a 22 MET cc_start: 0.8814 (mtt) cc_final: 0.8538 (mtt) REVERT: a 52 LYS cc_start: 0.8350 (mppt) cc_final: 0.7955 (mppt) REVERT: e 28 ASN cc_start: 0.7661 (OUTLIER) cc_final: 0.7441 (t0) REVERT: e 52 LYS cc_start: 0.8435 (mppt) cc_final: 0.8215 (mtmm) outliers start: 77 outliers final: 53 residues processed: 316 average time/residue: 0.3089 time to fit residues: 143.4581 Evaluate side-chains 299 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 237 time to evaluate : 1.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 137 MET Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 135 ASN Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 135 ASN Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 109 optimal weight: 0.3980 chunk 60 optimal weight: 5.9990 chunk 163 optimal weight: 7.9990 chunk 133 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 212 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 194 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 157 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 ASN G 148 ASN c 48 GLN e 28 ASN f 28 ASN ** f 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17397 Z= 0.242 Angle : 0.575 8.747 23598 Z= 0.310 Chirality : 0.045 0.151 2655 Planarity : 0.004 0.040 3123 Dihedral : 8.047 56.241 2441 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.68 % Favored : 91.32 % Rotamer: Outliers : 4.85 % Allowed : 17.64 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.66 (0.18), residues: 2178 helix: 0.66 (0.21), residues: 603 sheet: -0.81 (0.22), residues: 693 loop : -2.61 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 252 PHE 0.030 0.002 PHE e 31 TYR 0.010 0.001 TYR F 158 ARG 0.001 0.000 ARG F 213 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 217 time to evaluate : 1.886 Fit side-chains REVERT: A 215 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8341 (tp) REVERT: B 131 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7770 (mp) REVERT: B 164 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7463 (p0) REVERT: C 137 MET cc_start: 0.8087 (ttm) cc_final: 0.7565 (ttm) REVERT: C 139 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7181 (mm-30) REVERT: D 48 LYS cc_start: 0.7473 (mtpp) cc_final: 0.7152 (mttp) REVERT: D 59 GLU cc_start: 0.8175 (mt-10) cc_final: 0.7874 (mt-10) REVERT: D 139 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7140 (mm-30) REVERT: E 146 GLU cc_start: 0.7100 (tp30) cc_final: 0.6835 (tp30) REVERT: F 59 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7835 (mt-10) REVERT: F 139 GLU cc_start: 0.7346 (mm-30) cc_final: 0.7069 (mm-30) REVERT: F 225 GLU cc_start: 0.8369 (tt0) cc_final: 0.8114 (tt0) REVERT: F 240 ILE cc_start: 0.8820 (mm) cc_final: 0.8584 (mm) REVERT: H 131 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7859 (mp) REVERT: H 137 MET cc_start: 0.7985 (OUTLIER) cc_final: 0.7451 (ttm) REVERT: H 139 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7219 (mm-30) REVERT: H 164 ASP cc_start: 0.8002 (OUTLIER) cc_final: 0.7733 (p0) REVERT: H 225 GLU cc_start: 0.8389 (tt0) cc_final: 0.8058 (tt0) REVERT: I 48 LYS cc_start: 0.7757 (mtpp) cc_final: 0.7505 (mttm) REVERT: I 131 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7756 (mp) REVERT: I 139 GLU cc_start: 0.7678 (mm-30) cc_final: 0.7247 (mm-30) REVERT: I 213 ARG cc_start: 0.8629 (mmt-90) cc_final: 0.8318 (mpt180) REVERT: I 232 MET cc_start: 0.8638 (tpt) cc_final: 0.7853 (tpt) REVERT: a 22 MET cc_start: 0.8784 (mtt) cc_final: 0.8552 (mtt) REVERT: a 52 LYS cc_start: 0.8337 (mppt) cc_final: 0.7960 (mppt) REVERT: b 22 MET cc_start: 0.8749 (mtp) cc_final: 0.8437 (mtp) REVERT: d 22 MET cc_start: 0.8858 (mtp) cc_final: 0.8551 (mtt) REVERT: e 52 LYS cc_start: 0.8420 (mppt) cc_final: 0.8212 (mtmm) outliers start: 90 outliers final: 66 residues processed: 280 average time/residue: 0.3054 time to fit residues: 127.1496 Evaluate side-chains 283 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 210 time to evaluate : 2.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 141 SER Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 141 SER Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 216 GLU Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 141 SER Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 131 LEU Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 194 optimal weight: 0.9980 chunk 147 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 21 optimal weight: 0.1980 chunk 93 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 197 optimal weight: 1.9990 chunk 208 optimal weight: 0.4980 chunk 103 optimal weight: 6.9990 chunk 186 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN f 28 ASN f 48 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17397 Z= 0.204 Angle : 0.550 8.819 23598 Z= 0.295 Chirality : 0.044 0.148 2655 Planarity : 0.003 0.038 3123 Dihedral : 7.744 59.927 2436 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 4.85 % Allowed : 18.66 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.17 (0.18), residues: 2178 helix: 1.08 (0.21), residues: 603 sheet: -0.68 (0.23), residues: 594 loop : -2.07 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 252 PHE 0.028 0.002 PHE f 31 TYR 0.009 0.001 TYR C 158 ARG 0.001 0.000 ARG I 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 238 time to evaluate : 1.562 Fit side-chains REVERT: A 215 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8407 (tp) REVERT: B 131 LEU cc_start: 0.8069 (OUTLIER) cc_final: 0.7779 (mp) REVERT: B 164 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7470 (p0) REVERT: D 48 LYS cc_start: 0.7413 (mtpp) cc_final: 0.7077 (mttp) REVERT: D 139 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7071 (mm-30) REVERT: F 59 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7805 (mt-10) REVERT: F 139 GLU cc_start: 0.7236 (mm-30) cc_final: 0.7029 (mm-30) REVERT: G 131 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7598 (mp) REVERT: G 240 ILE cc_start: 0.8777 (mm) cc_final: 0.8538 (mt) REVERT: H 137 MET cc_start: 0.7975 (OUTLIER) cc_final: 0.7761 (ttm) REVERT: H 164 ASP cc_start: 0.7988 (OUTLIER) cc_final: 0.7720 (p0) REVERT: H 225 GLU cc_start: 0.8356 (tt0) cc_final: 0.8093 (tt0) REVERT: I 48 LYS cc_start: 0.7666 (mtpp) cc_final: 0.7346 (mttm) REVERT: I 131 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7740 (mp) REVERT: I 139 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7382 (mm-30) REVERT: I 213 ARG cc_start: 0.8636 (mmt-90) cc_final: 0.8329 (mpt180) REVERT: I 232 MET cc_start: 0.8635 (tpt) cc_final: 0.7981 (tpt) REVERT: a 22 MET cc_start: 0.8840 (mtt) cc_final: 0.8599 (mtt) REVERT: a 52 LYS cc_start: 0.8287 (mppt) cc_final: 0.7929 (mppt) REVERT: b 22 MET cc_start: 0.8749 (mtp) cc_final: 0.8437 (mtp) REVERT: e 52 LYS cc_start: 0.8394 (mppt) cc_final: 0.8181 (mtmm) outliers start: 90 outliers final: 67 residues processed: 296 average time/residue: 0.3115 time to fit residues: 138.2646 Evaluate side-chains 285 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 211 time to evaluate : 1.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 215 LEU Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 173 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 155 optimal weight: 5.9990 chunk 86 optimal weight: 5.9990 chunk 178 optimal weight: 6.9990 chunk 144 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 106 optimal weight: 6.9990 chunk 187 optimal weight: 5.9990 chunk 52 optimal weight: 4.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 135 ASN f 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17397 Z= 0.420 Angle : 0.655 8.096 23598 Z= 0.353 Chirality : 0.048 0.164 2655 Planarity : 0.004 0.039 3123 Dihedral : 8.022 59.270 2430 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.95 % Favored : 91.05 % Rotamer: Outliers : 6.20 % Allowed : 17.58 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.43 (0.18), residues: 2178 helix: 0.79 (0.21), residues: 603 sheet: -0.57 (0.22), residues: 684 loop : -2.51 (0.19), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 252 PHE 0.043 0.003 PHE i 31 TYR 0.017 0.001 TYR B 158 ARG 0.003 0.000 ARG f 27 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 232 time to evaluate : 1.674 Fit side-chains REVERT: A 107 GLU cc_start: 0.8600 (tp30) cc_final: 0.8379 (tp30) REVERT: A 215 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8321 (tp) REVERT: A 218 GLU cc_start: 0.7376 (pt0) cc_final: 0.7151 (pt0) REVERT: A 225 GLU cc_start: 0.8270 (tt0) cc_final: 0.7918 (tt0) REVERT: B 106 ASN cc_start: 0.7789 (m-40) cc_final: 0.7561 (m-40) REVERT: B 131 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7752 (mp) REVERT: B 215 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8216 (tp) REVERT: C 139 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7333 (mm-30) REVERT: D 107 GLU cc_start: 0.8566 (tp30) cc_final: 0.8287 (tp30) REVERT: D 131 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7841 (mp) REVERT: D 139 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7171 (mm-30) REVERT: E 215 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8537 (tp) REVERT: F 59 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7726 (mt-10) REVERT: F 107 GLU cc_start: 0.8427 (tp30) cc_final: 0.8222 (tp30) REVERT: F 139 GLU cc_start: 0.7422 (mm-30) cc_final: 0.7163 (mm-30) REVERT: F 240 ILE cc_start: 0.8861 (mm) cc_final: 0.8648 (mm) REVERT: G 131 LEU cc_start: 0.8195 (OUTLIER) cc_final: 0.7911 (mp) REVERT: G 215 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8514 (tp) REVERT: H 59 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7834 (mt-10) REVERT: I 48 LYS cc_start: 0.7714 (mtpp) cc_final: 0.7383 (mttm) REVERT: I 139 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7396 (mm-30) REVERT: I 213 ARG cc_start: 0.8710 (mmt-90) cc_final: 0.8466 (mpt180) REVERT: I 215 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8395 (tp) REVERT: I 232 MET cc_start: 0.8648 (tpt) cc_final: 0.7961 (tpt) REVERT: e 52 LYS cc_start: 0.8460 (mppt) cc_final: 0.8191 (mtmm) outliers start: 115 outliers final: 82 residues processed: 320 average time/residue: 0.3055 time to fit residues: 144.4311 Evaluate side-chains 317 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 227 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 243 ILE Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 135 ASN Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 137 MET Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 192 THR Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Chi-restraints excluded: chain h residue 50 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 70 optimal weight: 4.9990 chunk 188 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 173 optimal weight: 3.9990 chunk 96 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 69 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 57 GLN H 77 GLN f 28 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17397 Z= 0.226 Angle : 0.569 8.812 23598 Z= 0.305 Chirality : 0.045 0.150 2655 Planarity : 0.003 0.038 3123 Dihedral : 7.742 59.794 2429 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.13 % Favored : 91.87 % Rotamer: Outliers : 5.12 % Allowed : 19.53 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.99 (0.19), residues: 2178 helix: 1.18 (0.21), residues: 603 sheet: -0.48 (0.23), residues: 603 loop : -1.99 (0.19), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 252 PHE 0.029 0.002 PHE f 31 TYR 0.011 0.001 TYR F 158 ARG 0.002 0.000 ARG G 213 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 218 time to evaluate : 1.826 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8408 (tp) REVERT: A 225 GLU cc_start: 0.8230 (tt0) cc_final: 0.7855 (tt0) REVERT: B 106 ASN cc_start: 0.7744 (m-40) cc_final: 0.7518 (m-40) REVERT: B 131 LEU cc_start: 0.8180 (OUTLIER) cc_final: 0.7839 (mp) REVERT: B 164 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7488 (p0) REVERT: C 139 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7263 (mm-30) REVERT: C 170 ASP cc_start: 0.7901 (m-30) cc_final: 0.7615 (m-30) REVERT: D 131 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7810 (mp) REVERT: D 139 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7164 (mm-30) REVERT: D 164 ASP cc_start: 0.7870 (OUTLIER) cc_final: 0.7598 (p0) REVERT: E 109 LYS cc_start: 0.9124 (mtpt) cc_final: 0.8910 (mtpt) REVERT: E 139 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7324 (mm-30) REVERT: F 109 LYS cc_start: 0.9059 (mtpt) cc_final: 0.8824 (mtmt) REVERT: F 139 GLU cc_start: 0.7363 (mm-30) cc_final: 0.7086 (mm-30) REVERT: F 240 ILE cc_start: 0.8741 (mm) cc_final: 0.8492 (mm) REVERT: G 131 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7725 (mp) REVERT: H 137 MET cc_start: 0.8011 (ttp) cc_final: 0.7804 (ttp) REVERT: H 164 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7753 (p0) REVERT: H 225 GLU cc_start: 0.8328 (tt0) cc_final: 0.8008 (tt0) REVERT: I 48 LYS cc_start: 0.7487 (mtpp) cc_final: 0.7151 (mttm) REVERT: I 139 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7364 (mm-30) REVERT: I 213 ARG cc_start: 0.8635 (mmt-90) cc_final: 0.8421 (mpt180) REVERT: I 215 LEU cc_start: 0.8711 (OUTLIER) cc_final: 0.8450 (tp) REVERT: I 216 GLU cc_start: 0.7220 (OUTLIER) cc_final: 0.6962 (pt0) REVERT: I 232 MET cc_start: 0.8612 (tpt) cc_final: 0.7987 (tpt) REVERT: b 22 MET cc_start: 0.8798 (mtp) cc_final: 0.8528 (mtp) REVERT: d 22 MET cc_start: 0.8889 (mtp) cc_final: 0.8467 (mtt) outliers start: 95 outliers final: 72 residues processed: 288 average time/residue: 0.2969 time to fit residues: 127.2583 Evaluate side-chains 294 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 213 time to evaluate : 1.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 251 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 57 GLN Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain d residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 201 optimal weight: 0.9990 chunk 23 optimal weight: 7.9990 chunk 119 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 118 optimal weight: 0.9980 chunk 175 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 208 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 126 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 62 GLN C 175 ASN G 57 GLN f 28 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 17397 Z= 0.406 Angle : 0.646 8.037 23598 Z= 0.348 Chirality : 0.048 0.164 2655 Planarity : 0.004 0.038 3123 Dihedral : 8.005 59.489 2429 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.09 % Favored : 90.91 % Rotamer: Outliers : 5.61 % Allowed : 19.09 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -1.25 (0.18), residues: 2178 helix: 1.05 (0.20), residues: 603 sheet: -0.49 (0.22), residues: 693 loop : -2.48 (0.19), residues: 882 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 252 PHE 0.042 0.003 PHE f 31 TYR 0.016 0.001 TYR B 158 ARG 0.003 0.000 ARG G 207 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 214 time to evaluate : 2.262 Fit side-chains REVERT: A 107 GLU cc_start: 0.8586 (tp30) cc_final: 0.8350 (tp30) REVERT: A 215 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8396 (tt) REVERT: A 225 GLU cc_start: 0.8249 (tt0) cc_final: 0.7862 (tt0) REVERT: B 106 ASN cc_start: 0.7801 (m-40) cc_final: 0.7565 (m-40) REVERT: B 131 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7824 (mp) REVERT: B 164 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7434 (p0) REVERT: C 139 GLU cc_start: 0.7591 (mm-30) cc_final: 0.7351 (mm-30) REVERT: D 131 LEU cc_start: 0.8151 (OUTLIER) cc_final: 0.7923 (mp) REVERT: D 139 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7292 (mm-30) REVERT: E 109 LYS cc_start: 0.9115 (mtpt) cc_final: 0.8902 (mtpt) REVERT: E 139 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7378 (mm-30) REVERT: E 215 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8556 (tp) REVERT: F 59 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7750 (mt-10) REVERT: F 109 LYS cc_start: 0.9045 (mtpt) cc_final: 0.8832 (mtmt) REVERT: F 139 GLU cc_start: 0.7430 (mm-30) cc_final: 0.7167 (mm-30) REVERT: F 225 GLU cc_start: 0.8416 (tt0) cc_final: 0.8186 (tt0) REVERT: F 240 ILE cc_start: 0.8773 (mm) cc_final: 0.8541 (mm) REVERT: G 48 LYS cc_start: 0.7419 (mtpp) cc_final: 0.7041 (mttp) REVERT: G 131 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7884 (mp) REVERT: G 139 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7280 (mm-30) REVERT: G 215 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8517 (tp) REVERT: H 59 GLU cc_start: 0.8219 (mt-10) cc_final: 0.7862 (mt-10) REVERT: H 164 ASP cc_start: 0.8107 (OUTLIER) cc_final: 0.7819 (p0) REVERT: I 48 LYS cc_start: 0.7510 (mtpp) cc_final: 0.7140 (mttm) REVERT: I 139 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7217 (mm-30) REVERT: I 176 LEU cc_start: 0.8950 (OUTLIER) cc_final: 0.8723 (mt) REVERT: I 213 ARG cc_start: 0.8713 (mmt-90) cc_final: 0.8474 (mpt180) REVERT: I 215 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8415 (tp) REVERT: I 232 MET cc_start: 0.8593 (tpt) cc_final: 0.7957 (tpt) REVERT: e 52 LYS cc_start: 0.8460 (mppt) cc_final: 0.8259 (mtmm) outliers start: 104 outliers final: 79 residues processed: 292 average time/residue: 0.3168 time to fit residues: 138.6832 Evaluate side-chains 299 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 210 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 135 ASN Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 135 ASN Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 135 ASN Chi-restraints excluded: chain E residue 176 LEU Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 135 ASN Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 80 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 183 THR Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 135 ASN Chi-restraints excluded: chain I residue 141 SER Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 21 THR Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 128 optimal weight: 0.3980 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 6.9990 chunk 132 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 163 optimal weight: 6.9990 chunk 189 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 57 GLN f 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7988 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17397 Z= 0.212 Angle : 0.561 8.875 23598 Z= 0.301 Chirality : 0.045 0.151 2655 Planarity : 0.003 0.037 3123 Dihedral : 7.672 59.662 2429 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 4.53 % Allowed : 20.44 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.77 (0.19), residues: 2178 helix: 1.50 (0.21), residues: 603 sheet: -0.41 (0.23), residues: 603 loop : -1.92 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 252 PHE 0.029 0.002 PHE f 31 TYR 0.009 0.001 TYR B 158 ARG 0.002 0.000 ARG f 27 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 215 time to evaluate : 1.786 Fit side-chains REVERT: A 215 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8446 (tp) REVERT: A 225 GLU cc_start: 0.8172 (tt0) cc_final: 0.7803 (tt0) REVERT: B 106 ASN cc_start: 0.7787 (m-40) cc_final: 0.7578 (m-40) REVERT: B 131 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7896 (mp) REVERT: B 139 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7439 (mm-30) REVERT: B 164 ASP cc_start: 0.7908 (OUTLIER) cc_final: 0.7507 (p0) REVERT: C 139 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7276 (mm-30) REVERT: C 170 ASP cc_start: 0.7921 (m-30) cc_final: 0.7641 (m-30) REVERT: D 131 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7772 (mp) REVERT: D 139 GLU cc_start: 0.7486 (mm-30) cc_final: 0.7157 (mm-30) REVERT: E 215 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8546 (tp) REVERT: F 139 GLU cc_start: 0.7390 (mm-30) cc_final: 0.7105 (mm-30) REVERT: F 240 ILE cc_start: 0.8760 (mm) cc_final: 0.8539 (mm) REVERT: G 48 LYS cc_start: 0.7258 (mtpp) cc_final: 0.7029 (mttp) REVERT: G 131 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7676 (mp) REVERT: G 215 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8504 (tp) REVERT: H 137 MET cc_start: 0.7921 (ttm) cc_final: 0.7708 (ttm) REVERT: H 139 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7248 (mm-30) REVERT: H 164 ASP cc_start: 0.8033 (OUTLIER) cc_final: 0.7750 (p0) REVERT: H 225 GLU cc_start: 0.8311 (tt0) cc_final: 0.7988 (tt0) REVERT: I 139 GLU cc_start: 0.7600 (mm-30) cc_final: 0.7290 (mm-30) REVERT: I 176 LEU cc_start: 0.8869 (OUTLIER) cc_final: 0.8664 (mt) REVERT: I 213 ARG cc_start: 0.8631 (mmt-90) cc_final: 0.8419 (mpt180) REVERT: I 215 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8445 (tp) REVERT: I 216 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6953 (pt0) REVERT: I 232 MET cc_start: 0.8509 (tpt) cc_final: 0.7927 (tpt) REVERT: b 22 MET cc_start: 0.8812 (mtp) cc_final: 0.8548 (mtp) outliers start: 84 outliers final: 66 residues processed: 278 average time/residue: 0.2945 time to fit residues: 122.6788 Evaluate side-chains 281 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 204 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain B residue 251 LEU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain D residue 251 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain F residue 251 LEU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain d residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 152 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 175 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 193 optimal weight: 1.9990 chunk 127 optimal weight: 9.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17397 Z= 0.282 Angle : 0.583 8.312 23598 Z= 0.314 Chirality : 0.046 0.157 2655 Planarity : 0.004 0.036 3123 Dihedral : 7.693 59.715 2429 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.18 % Favored : 90.82 % Rotamer: Outliers : 4.75 % Allowed : 20.33 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.74 (0.19), residues: 2178 helix: 1.54 (0.21), residues: 603 sheet: -0.42 (0.23), residues: 603 loop : -1.89 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 252 PHE 0.032 0.002 PHE f 31 TYR 0.012 0.001 TYR G 158 ARG 0.002 0.000 ARG G 207 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 198 time to evaluate : 1.706 Fit side-chains revert: symmetry clash REVERT: A 215 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8439 (tp) REVERT: A 225 GLU cc_start: 0.8155 (tt0) cc_final: 0.7776 (tt0) REVERT: B 106 ASN cc_start: 0.7788 (m-40) cc_final: 0.7578 (m-40) REVERT: B 131 LEU cc_start: 0.8181 (OUTLIER) cc_final: 0.7833 (mp) REVERT: B 164 ASP cc_start: 0.7871 (OUTLIER) cc_final: 0.7451 (p0) REVERT: C 137 MET cc_start: 0.7656 (ttm) cc_final: 0.7261 (ttm) REVERT: C 139 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7262 (mm-30) REVERT: D 131 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7828 (mp) REVERT: D 139 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7162 (mm-30) REVERT: D 164 ASP cc_start: 0.7901 (OUTLIER) cc_final: 0.7631 (p0) REVERT: E 139 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7401 (mm-30) REVERT: E 215 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8563 (tp) REVERT: F 139 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7129 (mm-30) REVERT: G 48 LYS cc_start: 0.7252 (mtpp) cc_final: 0.7003 (mttp) REVERT: G 131 LEU cc_start: 0.8148 (OUTLIER) cc_final: 0.7760 (mp) REVERT: G 139 GLU cc_start: 0.7572 (mm-30) cc_final: 0.7303 (mm-30) REVERT: G 215 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8507 (tp) REVERT: H 164 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7788 (p0) REVERT: H 225 GLU cc_start: 0.8364 (tt0) cc_final: 0.8121 (tt0) REVERT: I 131 LEU cc_start: 0.8094 (OUTLIER) cc_final: 0.7864 (mp) REVERT: I 139 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7297 (mm-30) REVERT: I 176 LEU cc_start: 0.8918 (OUTLIER) cc_final: 0.8703 (mt) REVERT: I 213 ARG cc_start: 0.8683 (mmt-90) cc_final: 0.8458 (mpt180) REVERT: I 215 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8463 (tp) REVERT: I 232 MET cc_start: 0.8474 (tpt) cc_final: 0.7902 (tpt) REVERT: b 22 MET cc_start: 0.8841 (mtp) cc_final: 0.8541 (mtp) outliers start: 88 outliers final: 65 residues processed: 269 average time/residue: 0.2962 time to fit residues: 119.1032 Evaluate side-chains 275 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 198 time to evaluate : 1.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 141 SER Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 192 THR Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 154 VAL Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 60 THR Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 176 LEU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 205 optimal weight: 0.5980 chunk 125 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 142 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 198 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 132 optimal weight: 0.8980 chunk 105 optimal weight: 0.5980 chunk 136 optimal weight: 3.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17397 Z= 0.217 Angle : 0.557 8.576 23598 Z= 0.299 Chirality : 0.045 0.153 2655 Planarity : 0.003 0.035 3123 Dihedral : 7.532 59.423 2429 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 4.26 % Allowed : 20.77 % Favored : 74.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.54 (0.19), residues: 2178 helix: 1.83 (0.21), residues: 603 sheet: -0.37 (0.23), residues: 603 loop : -1.81 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 252 PHE 0.027 0.002 PHE f 31 TYR 0.010 0.001 TYR G 158 ARG 0.002 0.000 ARG B 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 217 time to evaluate : 1.791 Fit side-chains REVERT: A 215 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8419 (tp) REVERT: A 225 GLU cc_start: 0.8139 (tt0) cc_final: 0.7767 (tt0) REVERT: B 106 ASN cc_start: 0.7783 (m-40) cc_final: 0.7578 (m-40) REVERT: B 131 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7901 (mp) REVERT: B 139 GLU cc_start: 0.7640 (mm-30) cc_final: 0.7389 (mm-30) REVERT: B 164 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7514 (p0) REVERT: C 139 GLU cc_start: 0.7551 (mm-30) cc_final: 0.7275 (mm-30) REVERT: D 131 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7710 (mp) REVERT: D 139 GLU cc_start: 0.7496 (mm-30) cc_final: 0.7184 (mm-30) REVERT: D 164 ASP cc_start: 0.7864 (OUTLIER) cc_final: 0.7595 (p0) REVERT: E 139 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7375 (mm-30) REVERT: E 215 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8536 (tp) REVERT: F 139 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7096 (mm-30) REVERT: F 164 ASP cc_start: 0.7910 (OUTLIER) cc_final: 0.7696 (p0) REVERT: G 48 LYS cc_start: 0.7207 (mtpp) cc_final: 0.6970 (mttp) REVERT: G 131 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7625 (mp) REVERT: G 139 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7291 (mm-30) REVERT: G 215 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8510 (tp) REVERT: H 164 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7769 (p0) REVERT: H 225 GLU cc_start: 0.8303 (tt0) cc_final: 0.7975 (tt0) REVERT: I 131 LEU cc_start: 0.8043 (OUTLIER) cc_final: 0.7824 (mp) REVERT: I 139 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7265 (mm-30) REVERT: I 213 ARG cc_start: 0.8631 (mmt-90) cc_final: 0.8415 (mpt180) REVERT: I 215 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8435 (tp) REVERT: I 216 GLU cc_start: 0.7252 (OUTLIER) cc_final: 0.6946 (pt0) REVERT: I 232 MET cc_start: 0.8449 (tpt) cc_final: 0.7884 (tpt) REVERT: b 22 MET cc_start: 0.8809 (mtp) cc_final: 0.8536 (mtp) REVERT: g 52 LYS cc_start: 0.8393 (mppt) cc_final: 0.8171 (mtmm) outliers start: 79 outliers final: 60 residues processed: 273 average time/residue: 0.2833 time to fit residues: 116.0175 Evaluate side-chains 281 residues out of total 1854 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 208 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 60 THR Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 192 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 216 GLU Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 131 LEU Chi-restraints excluded: chain B residue 135 ASN Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 190 VAL Chi-restraints excluded: chain B residue 192 THR Chi-restraints excluded: chain B residue 198 SER Chi-restraints excluded: chain B residue 216 GLU Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 154 VAL Chi-restraints excluded: chain C residue 164 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 216 GLU Chi-restraints excluded: chain C residue 251 LEU Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 135 ASN Chi-restraints excluded: chain D residue 164 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 190 VAL Chi-restraints excluded: chain D residue 198 SER Chi-restraints excluded: chain D residue 215 LEU Chi-restraints excluded: chain D residue 216 GLU Chi-restraints excluded: chain E residue 164 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain F residue 60 THR Chi-restraints excluded: chain F residue 137 MET Chi-restraints excluded: chain F residue 164 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 192 THR Chi-restraints excluded: chain F residue 216 GLU Chi-restraints excluded: chain G residue 60 THR Chi-restraints excluded: chain G residue 131 LEU Chi-restraints excluded: chain G residue 137 MET Chi-restraints excluded: chain G residue 164 ASP Chi-restraints excluded: chain G residue 179 VAL Chi-restraints excluded: chain G residue 190 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 216 GLU Chi-restraints excluded: chain G residue 251 LEU Chi-restraints excluded: chain H residue 141 SER Chi-restraints excluded: chain H residue 164 ASP Chi-restraints excluded: chain H residue 179 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 192 THR Chi-restraints excluded: chain H residue 216 GLU Chi-restraints excluded: chain H residue 219 VAL Chi-restraints excluded: chain H residue 247 ILE Chi-restraints excluded: chain H residue 251 LEU Chi-restraints excluded: chain I residue 131 LEU Chi-restraints excluded: chain I residue 179 VAL Chi-restraints excluded: chain I residue 190 VAL Chi-restraints excluded: chain I residue 215 LEU Chi-restraints excluded: chain I residue 216 GLU Chi-restraints excluded: chain I residue 228 MET Chi-restraints excluded: chain I residue 247 ILE Chi-restraints excluded: chain I residue 251 LEU Chi-restraints excluded: chain a residue 28 ASN Chi-restraints excluded: chain f residue 28 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 158 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 176 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.132954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.112640 restraints weight = 18297.158| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.16 r_work: 0.3124 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17397 Z= 0.272 Angle : 0.579 8.290 23598 Z= 0.311 Chirality : 0.045 0.158 2655 Planarity : 0.004 0.035 3123 Dihedral : 7.520 59.420 2428 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 4.26 % Allowed : 20.93 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.55 (0.19), residues: 2178 helix: 1.80 (0.21), residues: 603 sheet: -0.39 (0.23), residues: 603 loop : -1.78 (0.20), residues: 972 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 252 PHE 0.030 0.002 PHE f 31 TYR 0.012 0.001 TYR B 158 ARG 0.002 0.000 ARG A 207 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3704.88 seconds wall clock time: 66 minutes 51.27 seconds (4011.27 seconds total)