Starting phenix.real_space_refine on Sat Sep 28 08:50:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/09_2024/7n6i_23726.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/09_2024/7n6i_23726.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/09_2024/7n6i_23726.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/09_2024/7n6i_23726.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/09_2024/7n6i_23726.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n6i_23726/09_2024/7n6i_23726.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 55 5.49 5 Mg 7 5.21 5 S 64 5.16 5 C 11744 2.51 5 N 3472 2.21 5 O 3597 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 81 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 18939 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 745 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 11, 'TRANS': 139} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 297 Chain: "B" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 745 Classifications: {'peptide': 151} Incomplete info: {'truncation_to_alanine': 125} Link IDs: {'PTRANS': 11, 'TRANS': 139} Unresolved chain link angles: 11 Unresolved non-hydrogen bonds: 499 Unresolved non-hydrogen angles: 637 Unresolved non-hydrogen dihedrals: 444 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'ASP:plan': 3, 'TYR:plan': 3, 'ASN:plan1': 3, 'TRP:plan': 5, 'HIS:plan': 7, 'PHE:plan': 7, 'GLU:plan': 11, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 297 Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 340 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "L" Number of atoms: 357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 357 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 11.60, per 1000 atoms: 0.61 Number of scatterers: 18939 At special positions: 0 Unit cell: (126.35, 143.64, 136.99, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 64 16.00 P 55 15.00 Mg 7 11.99 O 3597 8.00 N 3472 7.00 C 11744 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.89 Conformation dependent library (CDL) restraints added in 2.4 seconds 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4420 Finding SS restraints... Secondary structure from input PDB file: 116 helices and 16 sheets defined 57.7% alpha, 4.3% beta 14 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 6.41 Creating SS restraints... Processing helix chain 'A' and resid 21 through 33 Processing helix chain 'A' and resid 36 through 49 Processing helix chain 'A' and resid 61 through 74 removed outlier: 4.002A pdb=" N GLN A 65 " --> pdb=" O ARG A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 111 through 116 Processing helix chain 'A' and resid 141 through 146 Processing helix chain 'B' and resid 21 through 33 Processing helix chain 'B' and resid 36 through 49 Processing helix chain 'B' and resid 61 through 74 removed outlier: 4.002A pdb=" N GLN B 65 " --> pdb=" O ARG B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 107 Processing helix chain 'B' and resid 111 through 116 Processing helix chain 'B' and resid 141 through 146 Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 removed outlier: 4.659A pdb=" N ASP C 127 " --> pdb=" O SER C 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG C 128 " --> pdb=" O ASP C 124 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 174 through 181 removed outlier: 4.120A pdb=" N ALA C 178 " --> pdb=" O ASP C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.610A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 215 removed outlier: 3.523A pdb=" N LYS C 205 " --> pdb=" O GLY C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 257 Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 removed outlier: 4.007A pdb=" N ASP D 127 " --> pdb=" O SER D 123 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG D 128 " --> pdb=" O ASP D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 175 through 181 Processing helix chain 'D' and resid 183 through 188 Processing helix chain 'D' and resid 201 through 216 removed outlier: 3.522A pdb=" N LYS D 205 " --> pdb=" O GLY D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 257 Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 77 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU E 113 " --> pdb=" O ILE E 109 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 134 removed outlier: 3.598A pdb=" N ASP E 127 " --> pdb=" O SER E 123 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ARG E 128 " --> pdb=" O ASP E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 174 through 181 removed outlier: 4.126A pdb=" N ALA E 178 " --> pdb=" O ASP E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.511A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 215 removed outlier: 3.521A pdb=" N LYS E 205 " --> pdb=" O GLY E 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 238 removed outlier: 4.345A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 257 Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 77 Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.856A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 134 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 174 through 181 removed outlier: 4.110A pdb=" N ALA F 178 " --> pdb=" O ASP F 174 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.510A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 201 through 215 removed outlier: 3.521A pdb=" N LYS F 205 " --> pdb=" O GLY F 201 " (cutoff:3.500A) Processing helix chain 'F' and resid 226 through 238 removed outlier: 4.483A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 257 Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 134 removed outlier: 4.658A pdb=" N ASP G 127 " --> pdb=" O SER G 123 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG G 128 " --> pdb=" O ASP G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 174 through 181 removed outlier: 4.081A pdb=" N ALA G 178 " --> pdb=" O ASP G 174 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS G 205 " --> pdb=" O GLY G 201 " (cutoff:3.500A) Processing helix chain 'G' and resid 226 through 238 removed outlier: 4.488A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 257 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 Processing helix chain 'H' and resid 65 through 77 Processing helix chain 'H' and resid 101 through 113 removed outlier: 3.856A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 removed outlier: 3.599A pdb=" N ASP H 127 " --> pdb=" O SER H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 174 through 181 removed outlier: 4.111A pdb=" N ALA H 178 " --> pdb=" O ASP H 174 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.602A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS H 205 " --> pdb=" O GLY H 201 " (cutoff:3.500A) Processing helix chain 'H' and resid 226 through 238 removed outlier: 4.487A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 257 Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 36 through 53 removed outlier: 3.817A pdb=" N GLY I 48 " --> pdb=" O ASP I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 101 through 113 removed outlier: 3.858A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 134 removed outlier: 4.657A pdb=" N ASP I 127 " --> pdb=" O SER I 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG I 128 " --> pdb=" O ASP I 124 " (cutoff:3.500A) Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 174 through 181 removed outlier: 4.091A pdb=" N ALA I 178 " --> pdb=" O ASP I 174 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.533A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 215 removed outlier: 3.522A pdb=" N LYS I 205 " --> pdb=" O GLY I 201 " (cutoff:3.500A) Processing helix chain 'I' and resid 226 through 238 removed outlier: 4.490A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 257 Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'J' and resid 20 through 29 Processing helix chain 'J' and resid 36 through 53 Processing helix chain 'J' and resid 65 through 77 Processing helix chain 'J' and resid 101 through 113 removed outlier: 3.857A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 removed outlier: 4.657A pdb=" N ASP J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 128 " --> pdb=" O ASP J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 152 No H-bonds generated for 'chain 'J' and resid 150 through 152' Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 174 through 181 removed outlier: 4.118A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.527A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 215 removed outlier: 3.521A pdb=" N LYS J 205 " --> pdb=" O GLY J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 226 through 238 removed outlier: 4.481A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 257 Processing helix chain 'J' and resid 264 through 273 Processing sheet with id=AA1, first strand: chain 'C' and resid 171 through 173 removed outlier: 5.842A pdb=" N VAL C 58 " --> pdb=" O GLY C 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL C 92 " --> pdb=" O ILE C 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 172 through 173 removed outlier: 5.904A pdb=" N VAL D 58 " --> pdb=" O GLY D 172 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL D 92 " --> pdb=" O ILE D 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 171 through 172 removed outlier: 5.858A pdb=" N VAL E 58 " --> pdb=" O GLY E 172 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL E 92 " --> pdb=" O ILE E 142 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 171 through 172 removed outlier: 5.963A pdb=" N VAL F 58 " --> pdb=" O GLY F 172 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 91 through 94 removed outlier: 7.051A pdb=" N VAL F 92 " --> pdb=" O ILE F 142 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 171 through 172 removed outlier: 6.001A pdb=" N VAL G 58 " --> pdb=" O GLY G 172 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.649A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 171 through 172 removed outlier: 6.283A pdb=" N VAL H 58 " --> pdb=" O GLY H 172 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.650A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'I' and resid 171 through 172 removed outlier: 6.124A pdb=" N VAL I 58 " --> pdb=" O GLY I 172 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.651A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 171 through 172 removed outlier: 5.963A pdb=" N VAL J 58 " --> pdb=" O GLY J 172 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.637A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) 875 hydrogen bonds defined for protein. 2607 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 28 hydrogen bonds 56 hydrogen bond angles 0 basepair planarities 14 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 5.73 Time building geometry restraints manager: 5.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3118 1.31 - 1.44: 4801 1.44 - 1.56: 11152 1.56 - 1.69: 108 1.69 - 1.81: 96 Bond restraints: 19275 Sorted by residual: bond pdb=" C4 ATP J 300 " pdb=" C5 ATP J 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.79e+01 bond pdb=" C4 ATP E 300 " pdb=" C5 ATP E 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.78e+01 bond pdb=" C4 ATP I 300 " pdb=" C5 ATP I 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.75e+01 bond pdb=" C4 ATP H 300 " pdb=" C5 ATP H 300 " ideal model delta sigma weight residual 1.388 1.470 -0.082 1.00e-02 1.00e+04 6.66e+01 bond pdb=" C4 ATP F 300 " pdb=" C5 ATP F 300 " ideal model delta sigma weight residual 1.388 1.469 -0.081 1.00e-02 1.00e+04 6.64e+01 ... (remaining 19270 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.13: 25530 4.13 - 8.26: 577 8.26 - 12.39: 44 12.39 - 16.53: 2 16.53 - 20.66: 14 Bond angle restraints: 26167 Sorted by residual: angle pdb=" PB ATP E 300 " pdb=" O3B ATP E 300 " pdb=" PG ATP E 300 " ideal model delta sigma weight residual 139.87 119.21 20.66 1.00e+00 1.00e+00 4.27e+02 angle pdb=" PB ATP D 300 " pdb=" O3B ATP D 300 " pdb=" PG ATP D 300 " ideal model delta sigma weight residual 139.87 119.28 20.59 1.00e+00 1.00e+00 4.24e+02 angle pdb=" PB ATP H 300 " pdb=" O3B ATP H 300 " pdb=" PG ATP H 300 " ideal model delta sigma weight residual 139.87 119.34 20.53 1.00e+00 1.00e+00 4.22e+02 angle pdb=" PB ATP I 300 " pdb=" O3B ATP I 300 " pdb=" PG ATP I 300 " ideal model delta sigma weight residual 139.87 119.54 20.33 1.00e+00 1.00e+00 4.13e+02 angle pdb=" PB ATP G 300 " pdb=" O3B ATP G 300 " pdb=" PG ATP G 300 " ideal model delta sigma weight residual 139.87 119.88 19.99 1.00e+00 1.00e+00 4.00e+02 ... (remaining 26162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.41: 11463 31.41 - 62.81: 439 62.81 - 94.22: 70 94.22 - 125.63: 1 125.63 - 157.04: 3 Dihedral angle restraints: 11976 sinusoidal: 5152 harmonic: 6824 Sorted by residual: dihedral pdb=" N ARG B 30 " pdb=" C ARG B 30 " pdb=" CA ARG B 30 " pdb=" CB ARG B 30 " ideal model delta harmonic sigma weight residual 122.80 162.49 -39.69 0 2.50e+00 1.60e-01 2.52e+02 dihedral pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CA ARG A 30 " pdb=" CB ARG A 30 " ideal model delta harmonic sigma weight residual 122.80 162.46 -39.66 0 2.50e+00 1.60e-01 2.52e+02 dihedral pdb=" C ARG B 30 " pdb=" N ARG B 30 " pdb=" CA ARG B 30 " pdb=" CB ARG B 30 " ideal model delta harmonic sigma weight residual -122.60 -160.03 37.43 0 2.50e+00 1.60e-01 2.24e+02 ... (remaining 11973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.347: 2950 0.347 - 0.693: 34 0.693 - 1.040: 4 1.040 - 1.387: 0 1.387 - 1.733: 2 Chirality restraints: 2990 Sorted by residual: chirality pdb=" CA ARG B 30 " pdb=" N ARG B 30 " pdb=" C ARG B 30 " pdb=" CB ARG B 30 " both_signs ideal model delta sigma weight residual False 2.51 0.78 1.73 2.00e-01 2.50e+01 7.51e+01 chirality pdb=" CA ARG A 30 " pdb=" N ARG A 30 " pdb=" C ARG A 30 " pdb=" CB ARG A 30 " both_signs ideal model delta sigma weight residual False 2.51 0.78 1.73 2.00e-01 2.50e+01 7.50e+01 chirality pdb=" CA TYR A 116 " pdb=" N TYR A 116 " pdb=" C TYR A 116 " pdb=" CB TYR A 116 " both_signs ideal model delta sigma weight residual False 2.51 1.78 0.73 2.00e-01 2.50e+01 1.32e+01 ... (remaining 2987 not shown) Planarity restraints: 3205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET A 92 " -0.016 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C MET A 92 " 0.054 2.00e-02 2.50e+03 pdb=" O MET A 92 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN A 93 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 92 " -0.016 2.00e-02 2.50e+03 3.11e-02 9.66e+00 pdb=" C MET B 92 " 0.054 2.00e-02 2.50e+03 pdb=" O MET B 92 " -0.021 2.00e-02 2.50e+03 pdb=" N GLN B 93 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 138 " -0.012 2.00e-02 2.50e+03 2.48e-02 6.17e+00 pdb=" C VAL H 138 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL H 138 " -0.016 2.00e-02 2.50e+03 pdb=" N GLU H 139 " -0.014 2.00e-02 2.50e+03 ... (remaining 3202 not shown) Histogram of nonbonded interaction distances: 1.34 - 2.05: 13 2.05 - 2.76: 1887 2.76 - 3.47: 26265 3.47 - 4.19: 41735 4.19 - 4.90: 72993 Nonbonded interactions: 142893 Sorted by model distance: nonbonded pdb=" CB ARG B 155 " pdb=" NH2 ARG I 128 " model vdw 1.336 3.520 nonbonded pdb=" CB ARG B 155 " pdb=" CZ ARG I 128 " model vdw 1.350 3.670 nonbonded pdb=" OD2 ASP I 245 " pdb=" O2' ATP I 300 " model vdw 1.484 3.040 nonbonded pdb=" OD2 ASP E 245 " pdb=" O2' ATP E 300 " model vdw 1.584 3.040 nonbonded pdb=" CB HIS B 34 " pdb=" OE2 GLU H 131 " model vdw 1.701 3.440 ... (remaining 142888 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' } ncs_group { reference = chain 'C' selection = (chain 'D' and resid 19 through 275) selection = (chain 'E' and resid 19 through 275) selection = (chain 'F' and resid 19 through 275) selection = (chain 'G' and resid 19 through 275) selection = (chain 'H' and resid 19 through 275) selection = (chain 'I' and resid 19 through 275) selection = (chain 'J' and resid 19 through 275) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.030 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.160 Process input model: 45.890 Find NCS groups from input model: 0.880 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6175 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 : 0.014 0.082 19275 Z= 0.915 Angle : 1.720 20.658 26167 Z= 1.347 Chirality : 0.126 1.733 2990 Planarity : 0.006 0.057 3205 Dihedral : 16.033 157.036 7556 Min Nonbonded Distance : 1.336 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.10 % Favored : 97.73 % Rotamer: Outliers : 0.45 % Allowed : 3.07 % Favored : 96.48 % Cbeta Deviations : 1.18 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.16), residues: 2338 helix: -0.21 (0.13), residues: 1262 sheet: -0.04 (0.51), residues: 96 loop : -0.28 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP I 45 HIS 0.001 0.000 HIS G 43 PHE 0.007 0.001 PHE H 125 TYR 0.007 0.000 TYR E 75 ARG 0.003 0.000 ARG C 116 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 842 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 834 time to evaluate : 2.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LEU cc_start: 0.7134 (mt) cc_final: 0.6871 (mp) REVERT: C 39 VAL cc_start: 0.8217 (t) cc_final: 0.7998 (t) REVERT: C 42 LEU cc_start: 0.9103 (tp) cc_final: 0.8583 (tp) REVERT: C 194 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8253 (tt) REVERT: C 199 LEU cc_start: 0.7136 (mt) cc_final: 0.6832 (mt) REVERT: D 244 LEU cc_start: 0.8751 (tp) cc_final: 0.8527 (tt) REVERT: E 49 LYS cc_start: 0.8872 (mmtt) cc_final: 0.8667 (mptt) REVERT: E 133 LEU cc_start: 0.8473 (mt) cc_final: 0.8252 (mt) REVERT: E 240 TYR cc_start: 0.8769 (m-80) cc_final: 0.8505 (m-80) REVERT: F 38 GLN cc_start: 0.7982 (tp40) cc_final: 0.7622 (tp40) REVERT: F 45 TRP cc_start: 0.8591 (t60) cc_final: 0.8387 (t60) REVERT: F 70 CYS cc_start: 0.7889 (m) cc_final: 0.7463 (m) REVERT: F 164 LEU cc_start: 0.8028 (mt) cc_final: 0.7790 (mt) REVERT: F 183 ASP cc_start: 0.6544 (t70) cc_final: 0.6316 (t70) REVERT: H 41 THR cc_start: 0.8869 (m) cc_final: 0.8527 (m) REVERT: H 163 ASP cc_start: 0.6463 (m-30) cc_final: 0.5819 (m-30) REVERT: I 77 HIS cc_start: 0.5999 (m-70) cc_final: 0.5791 (m-70) REVERT: I 204 PHE cc_start: 0.8420 (t80) cc_final: 0.7889 (t80) REVERT: J 100 CYS cc_start: 0.1713 (t) cc_final: 0.1485 (t) REVERT: J 211 TRP cc_start: 0.6531 (t-100) cc_final: 0.5891 (t-100) outliers start: 8 outliers final: 1 residues processed: 838 average time/residue: 0.3716 time to fit residues: 449.9886 Evaluate side-chains 401 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 399 time to evaluate : 2.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 194 LEU Chi-restraints excluded: chain C residue 196 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 5.9990 chunk 175 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 118 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 181 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 chunk 135 optimal weight: 0.8980 chunk 210 optimal weight: 8.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 22 GLN C 185 GLN D 22 GLN D 77 HIS F 77 HIS F 185 GLN H 97 HIS I 38 GLN J 37 GLN J 98 GLN J 193 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6505 moved from start: 0.4433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19275 Z= 0.228 Angle : 0.716 13.234 26167 Z= 0.374 Chirality : 0.044 0.235 2990 Planarity : 0.005 0.051 3205 Dihedral : 16.518 154.912 3240 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 3.79 % Allowed : 16.63 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.17), residues: 2338 helix: 1.00 (0.14), residues: 1284 sheet: 0.23 (0.54), residues: 96 loop : 0.10 (0.20), residues: 958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP F 20 HIS 0.006 0.001 HIS J 193 PHE 0.031 0.002 PHE D 125 TYR 0.022 0.002 TYR F 112 ARG 0.008 0.001 ARG I 53 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 434 time to evaluate : 2.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 TYR cc_start: 0.8120 (m-10) cc_final: 0.7779 (m-10) REVERT: C 163 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7523 (p0) REVERT: C 187 LEU cc_start: 0.8535 (pp) cc_final: 0.7945 (tt) REVERT: C 199 LEU cc_start: 0.7295 (mt) cc_final: 0.7088 (mt) REVERT: D 159 ASP cc_start: 0.5652 (m-30) cc_final: 0.5428 (m-30) REVERT: D 187 LEU cc_start: 0.8276 (tp) cc_final: 0.7981 (tp) REVERT: E 224 LEU cc_start: 0.8432 (mt) cc_final: 0.8207 (mt) REVERT: E 233 LEU cc_start: 0.8856 (mt) cc_final: 0.8481 (mt) REVERT: F 70 CYS cc_start: 0.7905 (m) cc_final: 0.7577 (m) REVERT: F 160 ILE cc_start: 0.8830 (mm) cc_final: 0.8606 (mm) REVERT: G 42 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8926 (tp) REVERT: G 142 ILE cc_start: 0.9339 (mp) cc_final: 0.9089 (mt) REVERT: H 38 GLN cc_start: 0.7459 (tt0) cc_final: 0.7199 (tt0) REVERT: H 54 LYS cc_start: 0.8264 (tttp) cc_final: 0.7416 (tttp) REVERT: H 140 MET cc_start: 0.6339 (ttp) cc_final: 0.6122 (ttm) REVERT: H 196 PHE cc_start: 0.8184 (OUTLIER) cc_final: 0.7840 (t80) REVERT: H 237 THR cc_start: 0.8984 (OUTLIER) cc_final: 0.8620 (p) REVERT: I 106 PHE cc_start: 0.6483 (m-10) cc_final: 0.5880 (m-10) REVERT: I 194 LEU cc_start: 0.8517 (tp) cc_final: 0.8308 (tt) REVERT: I 199 LEU cc_start: 0.6634 (tp) cc_final: 0.6376 (tp) REVERT: I 250 GLU cc_start: 0.6844 (tt0) cc_final: 0.6567 (tt0) REVERT: J 98 GLN cc_start: 0.7086 (tp-100) cc_final: 0.6597 (tp-100) outliers start: 68 outliers final: 30 residues processed: 481 average time/residue: 0.3028 time to fit residues: 217.9999 Evaluate side-chains 370 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 336 time to evaluate : 2.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 163 ASP Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 221 SER Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 109 ILE Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 216 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 203 ASP Chi-restraints excluded: chain H residue 237 THR Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 208 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 117 optimal weight: 0.6980 chunk 65 optimal weight: 6.9990 chunk 175 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 211 optimal weight: 0.1980 chunk 228 optimal weight: 6.9990 chunk 187 optimal weight: 0.0370 chunk 209 optimal weight: 20.0000 chunk 71 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 overall best weight: 0.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 GLN E 38 GLN I 38 GLN I 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6546 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19275 Z= 0.199 Angle : 0.645 12.104 26167 Z= 0.337 Chirality : 0.042 0.242 2990 Planarity : 0.005 0.046 3205 Dihedral : 16.307 153.999 3238 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.85 % Allowed : 19.36 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2338 helix: 1.20 (0.14), residues: 1292 sheet: 0.19 (0.53), residues: 96 loop : 0.24 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 20 HIS 0.007 0.001 HIS I 77 PHE 0.041 0.002 PHE I 125 TYR 0.016 0.001 TYR F 112 ARG 0.008 0.000 ARG H 258 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 375 time to evaluate : 2.059 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 TYR cc_start: 0.8152 (m-80) cc_final: 0.7856 (m-10) REVERT: C 229 MET cc_start: 0.4287 (pmm) cc_final: 0.3852 (pmm) REVERT: E 179 VAL cc_start: 0.9062 (t) cc_final: 0.8797 (p) REVERT: E 224 LEU cc_start: 0.8424 (mt) cc_final: 0.8174 (mt) REVERT: G 142 ILE cc_start: 0.9368 (mp) cc_final: 0.9098 (mt) REVERT: H 159 ASP cc_start: 0.6709 (t0) cc_final: 0.5980 (t0) REVERT: I 194 LEU cc_start: 0.8548 (tp) cc_final: 0.8297 (tt) REVERT: I 199 LEU cc_start: 0.6633 (tp) cc_final: 0.6372 (tp) REVERT: J 166 ILE cc_start: 0.5105 (OUTLIER) cc_final: 0.4791 (tt) outliers start: 51 outliers final: 30 residues processed: 413 average time/residue: 0.2836 time to fit residues: 181.9355 Evaluate side-chains 354 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 323 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 133 LEU Chi-restraints excluded: chain H residue 91 VAL Chi-restraints excluded: chain H residue 113 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 196 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 208 optimal weight: 9.9990 chunk 158 optimal weight: 0.0970 chunk 109 optimal weight: 5.9990 chunk 23 optimal weight: 50.0000 chunk 100 optimal weight: 0.4980 chunk 141 optimal weight: 6.9990 chunk 211 optimal weight: 0.0010 chunk 224 optimal weight: 8.9990 chunk 110 optimal weight: 0.9980 chunk 200 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 overall best weight: 0.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 38 GLN E 77 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 37 GLN H 38 GLN I 38 GLN I 185 GLN J 38 GLN ** J 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.5590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19275 Z= 0.178 Angle : 0.648 13.104 26167 Z= 0.333 Chirality : 0.043 0.281 2990 Planarity : 0.004 0.043 3205 Dihedral : 16.126 153.475 3238 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.12 % Allowed : 19.20 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2338 helix: 1.22 (0.14), residues: 1292 sheet: 0.23 (0.53), residues: 96 loop : 0.26 (0.20), residues: 950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 20 HIS 0.005 0.001 HIS I 77 PHE 0.048 0.002 PHE J 154 TYR 0.015 0.001 TYR F 112 ARG 0.005 0.000 ARG G 175 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 356 time to evaluate : 2.183 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 115 TYR cc_start: 0.8174 (m-80) cc_final: 0.7887 (m-10) REVERT: D 250 GLU cc_start: 0.6510 (tt0) cc_final: 0.6302 (tt0) REVERT: E 163 ASP cc_start: 0.6235 (p0) cc_final: 0.5923 (p0) REVERT: E 179 VAL cc_start: 0.8980 (t) cc_final: 0.8724 (p) REVERT: E 224 LEU cc_start: 0.8493 (mt) cc_final: 0.8168 (mt) REVERT: F 145 GLU cc_start: 0.7347 (tt0) cc_final: 0.7113 (tm-30) REVERT: G 142 ILE cc_start: 0.9350 (mp) cc_final: 0.9105 (mt) REVERT: G 213 GLN cc_start: 0.5994 (tm-30) cc_final: 0.5762 (tm-30) REVERT: G 214 MET cc_start: 0.5858 (mmm) cc_final: 0.5504 (mmm) REVERT: H 159 ASP cc_start: 0.6827 (t0) cc_final: 0.6600 (t0) REVERT: I 194 LEU cc_start: 0.8555 (tp) cc_final: 0.8165 (tt) REVERT: J 166 ILE cc_start: 0.5056 (OUTLIER) cc_final: 0.4783 (tt) outliers start: 56 outliers final: 40 residues processed: 391 average time/residue: 0.2800 time to fit residues: 169.9652 Evaluate side-chains 358 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 317 time to evaluate : 2.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 218 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 38 GLN Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 38 GLN Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 166 ILE Chi-restraints excluded: chain J residue 196 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 186 optimal weight: 0.0970 chunk 127 optimal weight: 3.9990 chunk 3 optimal weight: 50.0000 chunk 166 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 191 optimal weight: 3.9990 chunk 155 optimal weight: 4.9990 chunk 0 optimal weight: 30.0000 chunk 114 optimal weight: 1.9990 chunk 201 optimal weight: 3.9990 chunk 56 optimal weight: 0.0070 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 38 GLN I 38 GLN I 77 HIS J 38 GLN J 97 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.5990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19275 Z= 0.218 Angle : 0.634 12.149 26167 Z= 0.332 Chirality : 0.042 0.292 2990 Planarity : 0.004 0.040 3205 Dihedral : 15.837 153.471 3238 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.52 % Allowed : 20.20 % Favored : 76.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.17), residues: 2338 helix: 1.21 (0.14), residues: 1300 sheet: -0.01 (0.52), residues: 96 loop : 0.28 (0.20), residues: 942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 20 HIS 0.009 0.001 HIS G 77 PHE 0.044 0.002 PHE I 125 TYR 0.019 0.001 TYR F 112 ARG 0.006 0.000 ARG F 148 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 327 time to evaluate : 2.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.2587 (mmtm) cc_final: 0.2028 (mmtm) REVERT: C 115 TYR cc_start: 0.8316 (m-80) cc_final: 0.8082 (m-10) REVERT: E 49 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8356 (mppt) REVERT: E 179 VAL cc_start: 0.8914 (t) cc_final: 0.8693 (p) REVERT: E 229 MET cc_start: 0.4976 (mmt) cc_final: 0.4694 (mmt) REVERT: F 145 GLU cc_start: 0.7696 (tt0) cc_final: 0.7190 (tm-30) REVERT: F 229 MET cc_start: 0.7137 (pmm) cc_final: 0.6913 (pmm) REVERT: G 142 ILE cc_start: 0.9358 (mp) cc_final: 0.9141 (mt) REVERT: G 213 GLN cc_start: 0.6135 (tm-30) cc_final: 0.5450 (tm-30) REVERT: G 214 MET cc_start: 0.5976 (mmm) cc_final: 0.5515 (mmm) REVERT: G 268 LEU cc_start: 0.8425 (mt) cc_final: 0.8163 (tp) REVERT: H 97 HIS cc_start: 0.7592 (m-70) cc_final: 0.7298 (m-70) REVERT: H 229 MET cc_start: 0.6734 (mmt) cc_final: 0.6471 (mmt) outliers start: 63 outliers final: 46 residues processed: 367 average time/residue: 0.2823 time to fit residues: 161.9087 Evaluate side-chains 346 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 299 time to evaluate : 2.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 133 LEU Chi-restraints excluded: chain D residue 156 ASP Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 196 PHE Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 248 LEU Chi-restraints excluded: chain G residue 42 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 208 VAL Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 229 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 75 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 131 optimal weight: 0.6980 chunk 55 optimal weight: 10.0000 chunk 224 optimal weight: 0.7980 chunk 186 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 18 optimal weight: 40.0000 chunk 74 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS ** F 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN J 97 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.6292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 19275 Z= 0.175 Angle : 0.642 12.947 26167 Z= 0.332 Chirality : 0.043 0.209 2990 Planarity : 0.004 0.043 3205 Dihedral : 15.603 153.556 3238 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.52 % Allowed : 21.09 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.17), residues: 2338 helix: 1.19 (0.15), residues: 1304 sheet: 0.09 (0.40), residues: 192 loop : 0.25 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 20 HIS 0.005 0.001 HIS E 77 PHE 0.045 0.002 PHE I 125 TYR 0.014 0.001 TYR F 112 ARG 0.006 0.000 ARG I 50 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 332 time to evaluate : 2.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3534 (mmtm) cc_final: 0.3194 (mmtm) REVERT: C 115 TYR cc_start: 0.8281 (m-80) cc_final: 0.7973 (m-10) REVERT: C 229 MET cc_start: 0.4627 (pmm) cc_final: 0.4397 (pmm) REVERT: E 49 LYS cc_start: 0.8588 (OUTLIER) cc_final: 0.8243 (mppt) REVERT: E 179 VAL cc_start: 0.8915 (t) cc_final: 0.8670 (p) REVERT: E 268 LEU cc_start: 0.8695 (pp) cc_final: 0.8433 (pp) REVERT: F 145 GLU cc_start: 0.7703 (tt0) cc_final: 0.7174 (tm-30) REVERT: G 142 ILE cc_start: 0.9351 (mp) cc_final: 0.9119 (mt) REVERT: G 268 LEU cc_start: 0.8363 (mt) cc_final: 0.8158 (tp) REVERT: H 97 HIS cc_start: 0.7569 (m-70) cc_final: 0.7293 (m170) outliers start: 63 outliers final: 39 residues processed: 374 average time/residue: 0.2865 time to fit residues: 165.9079 Evaluate side-chains 343 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 303 time to evaluate : 2.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 196 PHE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 113 LEU Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 263 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 213 GLN Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain H residue 253 ILE Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 250 GLU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 216 optimal weight: 10.0000 chunk 25 optimal weight: 8.9990 chunk 127 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 188 optimal weight: 2.9990 chunk 125 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 139 optimal weight: 0.7980 chunk 136 optimal weight: 0.0060 chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 0.9980 overall best weight: 0.9198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS ** J 38 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6675 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19275 Z= 0.193 Angle : 0.662 12.720 26167 Z= 0.339 Chirality : 0.043 0.248 2990 Planarity : 0.004 0.038 3205 Dihedral : 15.414 153.688 3238 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.35 % Allowed : 21.71 % Favored : 74.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.17), residues: 2338 helix: 1.19 (0.15), residues: 1296 sheet: 0.02 (0.40), residues: 192 loop : 0.23 (0.21), residues: 850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP J 211 HIS 0.004 0.001 HIS E 77 PHE 0.044 0.002 PHE I 125 TYR 0.017 0.001 TYR J 75 ARG 0.004 0.000 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 330 time to evaluate : 2.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3375 (mmtm) cc_final: 0.2656 (tptm) REVERT: C 229 MET cc_start: 0.4851 (pmm) cc_final: 0.4278 (pmm) REVERT: E 49 LYS cc_start: 0.8591 (OUTLIER) cc_final: 0.8255 (mppt) REVERT: E 163 ASP cc_start: 0.6458 (p0) cc_final: 0.6032 (p0) REVERT: E 179 VAL cc_start: 0.8691 (t) cc_final: 0.8440 (p) REVERT: E 185 GLN cc_start: 0.6930 (tp-100) cc_final: 0.6619 (tp-100) REVERT: F 145 GLU cc_start: 0.7716 (tt0) cc_final: 0.7206 (tm-30) REVERT: F 204 PHE cc_start: 0.7796 (t80) cc_final: 0.7536 (t80) REVERT: F 229 MET cc_start: 0.7632 (pmm) cc_final: 0.7151 (pmm) REVERT: G 142 ILE cc_start: 0.9343 (mp) cc_final: 0.9119 (mt) REVERT: G 268 LEU cc_start: 0.8497 (mt) cc_final: 0.8252 (tp) REVERT: H 97 HIS cc_start: 0.7615 (m-70) cc_final: 0.7327 (m170) REVERT: H 180 ILE cc_start: 0.9198 (tt) cc_final: 0.8970 (pt) outliers start: 60 outliers final: 40 residues processed: 369 average time/residue: 0.2856 time to fit residues: 162.6926 Evaluate side-chains 341 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 300 time to evaluate : 2.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain C residue 250 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 246 GLU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 203 ASP Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 179 VAL Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 89 optimal weight: 0.9980 chunk 133 optimal weight: 4.9990 chunk 67 optimal weight: 0.3980 chunk 43 optimal weight: 1.9990 chunk 142 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 20 optimal weight: 40.0000 chunk 175 optimal weight: 2.9990 chunk 203 optimal weight: 4.9990 chunk 214 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 213 GLN E 77 HIS J 97 HIS ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.6874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19275 Z= 0.218 Angle : 0.698 15.091 26167 Z= 0.357 Chirality : 0.043 0.231 2990 Planarity : 0.004 0.057 3205 Dihedral : 15.265 154.036 3236 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.18 % Allowed : 22.15 % Favored : 74.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2338 helix: 1.09 (0.15), residues: 1304 sheet: -0.32 (0.53), residues: 96 loop : 0.24 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 211 HIS 0.004 0.001 HIS E 77 PHE 0.043 0.002 PHE I 125 TYR 0.018 0.001 TYR F 112 ARG 0.005 0.000 ARG G 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 308 time to evaluate : 2.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3495 (mmtm) cc_final: 0.2519 (tptm) REVERT: C 229 MET cc_start: 0.4963 (pmm) cc_final: 0.4329 (pmm) REVERT: D 187 LEU cc_start: 0.8466 (mt) cc_final: 0.8038 (mt) REVERT: E 49 LYS cc_start: 0.8668 (OUTLIER) cc_final: 0.8314 (mppt) REVERT: E 54 LYS cc_start: 0.8447 (tttt) cc_final: 0.7572 (tttt) REVERT: E 163 ASP cc_start: 0.6626 (p0) cc_final: 0.6144 (p0) REVERT: E 179 VAL cc_start: 0.8666 (t) cc_final: 0.8393 (p) REVERT: E 185 GLN cc_start: 0.7223 (tp-100) cc_final: 0.6790 (tp-100) REVERT: F 145 GLU cc_start: 0.7831 (tt0) cc_final: 0.7355 (tm-30) REVERT: F 204 PHE cc_start: 0.7951 (t80) cc_final: 0.7704 (t80) REVERT: F 229 MET cc_start: 0.7389 (pmm) cc_final: 0.7005 (pmm) REVERT: F 268 LEU cc_start: 0.9185 (mt) cc_final: 0.8944 (mt) REVERT: G 142 ILE cc_start: 0.9345 (mp) cc_final: 0.9119 (mt) REVERT: G 268 LEU cc_start: 0.8531 (mt) cc_final: 0.8267 (tp) REVERT: H 97 HIS cc_start: 0.7476 (m-70) cc_final: 0.7262 (m170) outliers start: 57 outliers final: 43 residues processed: 343 average time/residue: 0.2759 time to fit residues: 148.1388 Evaluate side-chains 333 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 289 time to evaluate : 2.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 ILE Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 247 ILE Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 269 GLN Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 49 LYS Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 218 LEU Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 127 ASP Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 168 VAL Chi-restraints excluded: chain I residue 208 VAL Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 196 PHE Chi-restraints excluded: chain J residue 267 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 195 optimal weight: 2.9990 chunk 208 optimal weight: 0.8980 chunk 214 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 90 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 188 optimal weight: 0.8980 chunk 197 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS J 97 HIS ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.7167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19275 Z= 0.221 Angle : 0.706 14.899 26167 Z= 0.361 Chirality : 0.044 0.239 2990 Planarity : 0.004 0.037 3205 Dihedral : 15.181 154.464 3236 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.68 % Allowed : 23.60 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.18), residues: 2338 helix: 1.08 (0.15), residues: 1304 sheet: -0.11 (0.40), residues: 192 loop : 0.25 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 211 HIS 0.004 0.001 HIS E 77 PHE 0.043 0.002 PHE I 125 TYR 0.021 0.001 TYR J 73 ARG 0.007 0.000 ARG I 182 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 294 time to evaluate : 2.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3553 (mmtm) cc_final: 0.2061 (tptp) REVERT: C 229 MET cc_start: 0.5101 (pmm) cc_final: 0.4506 (pmm) REVERT: D 187 LEU cc_start: 0.8489 (mt) cc_final: 0.8220 (mt) REVERT: E 163 ASP cc_start: 0.6703 (p0) cc_final: 0.6236 (p0) REVERT: E 185 GLN cc_start: 0.7066 (tp-100) cc_final: 0.6648 (tp-100) REVERT: F 145 GLU cc_start: 0.7948 (tt0) cc_final: 0.7526 (tm-30) REVERT: F 204 PHE cc_start: 0.7961 (t80) cc_final: 0.7686 (t80) REVERT: F 229 MET cc_start: 0.7460 (pmm) cc_final: 0.7105 (pmm) REVERT: G 142 ILE cc_start: 0.9337 (mp) cc_final: 0.9135 (mt) REVERT: G 268 LEU cc_start: 0.8509 (mt) cc_final: 0.8301 (tp) outliers start: 48 outliers final: 36 residues processed: 326 average time/residue: 0.2747 time to fit residues: 141.7820 Evaluate side-chains 314 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 278 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 221 SER Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 138 VAL Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 213 GLN Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain F residue 224 LEU Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 248 LEU Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 220 optimal weight: 4.9990 chunk 134 optimal weight: 0.1980 chunk 104 optimal weight: 0.0870 chunk 153 optimal weight: 0.9990 chunk 231 optimal weight: 10.0000 chunk 212 optimal weight: 0.9980 chunk 184 optimal weight: 2.9990 chunk 19 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 146 optimal weight: 1.9990 overall best weight: 0.6360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 77 HIS H 80 GLN ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.7342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 19275 Z= 0.193 Angle : 0.731 16.267 26167 Z= 0.369 Chirality : 0.044 0.232 2990 Planarity : 0.004 0.040 3205 Dihedral : 15.070 154.590 3236 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.29 % Allowed : 24.61 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.18), residues: 2338 helix: 1.05 (0.15), residues: 1296 sheet: -0.52 (0.51), residues: 96 loop : 0.15 (0.20), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 20 HIS 0.005 0.001 HIS E 77 PHE 0.043 0.002 PHE I 125 TYR 0.018 0.001 TYR J 75 ARG 0.007 0.000 ARG E 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4676 Ramachandran restraints generated. 2338 Oldfield, 0 Emsley, 2338 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 289 time to evaluate : 2.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 LYS cc_start: 0.3533 (mmtm) cc_final: 0.2669 (tptp) REVERT: C 131 GLU cc_start: 0.7032 (tm-30) cc_final: 0.6832 (tm-30) REVERT: C 229 MET cc_start: 0.5003 (pmm) cc_final: 0.4284 (pmm) REVERT: D 187 LEU cc_start: 0.8466 (mt) cc_final: 0.8126 (mt) REVERT: E 163 ASP cc_start: 0.6777 (p0) cc_final: 0.6211 (p0) REVERT: E 179 VAL cc_start: 0.8483 (t) cc_final: 0.8278 (p) REVERT: E 185 GLN cc_start: 0.7102 (tp-100) cc_final: 0.6657 (tp-100) REVERT: F 145 GLU cc_start: 0.7893 (tt0) cc_final: 0.7544 (tm-30) REVERT: F 204 PHE cc_start: 0.7889 (t80) cc_final: 0.7628 (t80) REVERT: F 229 MET cc_start: 0.7452 (pmm) cc_final: 0.7139 (pmm) REVERT: G 268 LEU cc_start: 0.8474 (mt) cc_final: 0.8254 (tp) outliers start: 41 outliers final: 32 residues processed: 315 average time/residue: 0.2872 time to fit residues: 144.2686 Evaluate side-chains 301 residues out of total 2042 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 269 time to evaluate : 2.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 113 LEU Chi-restraints excluded: chain C residue 171 VAL Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 248 LEU Chi-restraints excluded: chain D residue 75 TYR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 119 LYS Chi-restraints excluded: chain D residue 171 VAL Chi-restraints excluded: chain D residue 183 ASP Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain E residue 21 LEU Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 253 ILE Chi-restraints excluded: chain F residue 64 THR Chi-restraints excluded: chain F residue 111 GLU Chi-restraints excluded: chain F residue 117 VAL Chi-restraints excluded: chain F residue 156 ASP Chi-restraints excluded: chain F residue 199 LEU Chi-restraints excluded: chain F residue 215 VAL Chi-restraints excluded: chain H residue 80 GLN Chi-restraints excluded: chain H residue 176 LEU Chi-restraints excluded: chain I residue 70 CYS Chi-restraints excluded: chain I residue 113 LEU Chi-restraints excluded: chain I residue 115 TYR Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 227 LYS Chi-restraints excluded: chain I residue 269 GLN Chi-restraints excluded: chain J residue 32 SER Chi-restraints excluded: chain J residue 34 VAL Chi-restraints excluded: chain J residue 89 VAL Chi-restraints excluded: chain J residue 196 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 232 random chunks: chunk 196 optimal weight: 6.9990 chunk 56 optimal weight: 0.7980 chunk 169 optimal weight: 3.9990 chunk 27 optimal weight: 30.0000 chunk 51 optimal weight: 4.9990 chunk 184 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 189 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 223 ASN E 77 HIS ** J 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.102447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.070948 restraints weight = 63069.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.073104 restraints weight = 34612.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.074534 restraints weight = 23593.339| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.7559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 19275 Z= 0.256 Angle : 0.757 15.873 26167 Z= 0.387 Chirality : 0.044 0.227 2990 Planarity : 0.004 0.055 3205 Dihedral : 15.023 155.036 3236 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.23 % Allowed : 25.22 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.18), residues: 2338 helix: 1.03 (0.15), residues: 1308 sheet: -0.48 (0.34), residues: 232 loop : 0.18 (0.22), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 211 HIS 0.004 0.001 HIS E 77 PHE 0.042 0.002 PHE I 125 TYR 0.022 0.001 TYR F 112 ARG 0.005 0.000 ARG I 182 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4171.24 seconds wall clock time: 76 minutes 4.34 seconds (4564.34 seconds total)