Starting phenix.real_space_refine on Sun Mar 24 23:05:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z16_14442/03_2024/7z16_14442_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z16_14442/03_2024/7z16_14442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z16_14442/03_2024/7z16_14442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z16_14442/03_2024/7z16_14442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z16_14442/03_2024/7z16_14442_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7z16_14442/03_2024/7z16_14442_neut_trim_updated.pdb" } resolution = 2.09 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= 0.003 sd= 0.127 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: 8 Type Number sf(0) Gaussians Zn 4 6.06 5 P 8 5.49 5 Mg 2 5.21 5 S 96 5.16 5 C 14074 2.51 5 N 4006 2.21 5 O 4260 1.98 5 H 22240 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44690 Number of models: 1 Model: "" Number of chains: 20 Chain: "A" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2187 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "B" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2956 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "C" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "D" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4357 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "E" Number of atoms: 2187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2187 Classifications: {'peptide': 143} Link IDs: {'PTRANS': 2, 'TRANS': 140} Chain: "F" Number of atoms: 2956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 2956 Classifications: {'peptide': 193} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 12, 'TRANS': 178} Chain: "G" Number of atoms: 5395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 5395 Classifications: {'peptide': 353} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 332} Chain: "H" Number of atoms: 4357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 4357 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 20, 'TRANS': 257} Chain: "I" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3899 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 3899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 3899 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 11, 'TRANS': 238} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "K" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3503 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "L" Number of atoms: 3503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 3503 Classifications: {'peptide': 224} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 11, 'TRANS': 212} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 6 Unusual residues: {' ZN': 1, 'PO4': 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, 'ANP': 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, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 9 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14336 SG CYS D 241 40.982 105.150 105.378 1.00 23.38 S ATOM 14375 SG CYS D 244 42.954 108.356 104.773 1.00 24.42 S ATOM 14695 SG CYS D 266 44.401 105.071 103.784 1.00 20.80 S ATOM 14775 SG CYS D 272 43.856 105.870 107.579 1.00 23.09 S ATOM 29231 SG CYS H 241 73.634 20.939 105.376 1.00 23.36 S ATOM 29270 SG CYS H 244 71.664 17.731 104.771 1.00 24.37 S ATOM 29590 SG CYS H 266 70.215 21.016 103.782 1.00 20.77 S ATOM 29670 SG CYS H 272 70.760 20.216 107.577 1.00 23.05 S Time building chain proxies: 17.51, per 1000 atoms: 0.39 Number of scatterers: 44690 At special positions: 0 Unit cell: (114.611, 127.028, 157.591, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Zn 4 29.99 S 96 16.00 P 8 15.00 Mg 2 11.99 O 4260 8.00 N 4006 7.00 C 14074 6.00 H 22240 1.00 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 39.63 Conformation dependent library (CDL) restraints added in 4.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1000 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 328 " pdb="ZN ZN C1000 " - pdb=" NE2 HIS C 333 " pdb=" ZN D1000 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 241 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 244 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 266 " pdb="ZN ZN D1000 " - pdb=" SG CYS D 272 " pdb=" ZN G1000 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 328 " pdb="ZN ZN G1000 " - pdb=" NE2 HIS G 333 " pdb=" ZN H1000 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 241 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 266 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 244 " pdb="ZN ZN H1000 " - pdb=" SG CYS H 272 " Number of angles added : 12 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5356 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 30 sheets defined 38.6% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.46 Creating SS restraints... Processing helix chain 'A' and resid 4 through 17 Processing helix chain 'A' and resid 20 through 30 Processing helix chain 'A' and resid 53 through 55 No H-bonds generated for 'chain 'A' and resid 53 through 55' Processing helix chain 'A' and resid 89 through 102 Processing helix chain 'A' and resid 105 through 114 removed outlier: 4.422A pdb=" N GLN A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ASN A 110 " --> pdb=" O ARG A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 137 removed outlier: 3.683A pdb=" N ALA A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER A 137 " --> pdb=" O GLU A 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 26 Processing helix chain 'B' and resid 46 through 55 Processing helix chain 'B' and resid 66 through 68 No H-bonds generated for 'chain 'B' and resid 66 through 68' Processing helix chain 'B' and resid 71 through 80 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 103 through 108 Processing helix chain 'B' and resid 155 through 163 Processing helix chain 'C' and resid 8 through 24 Processing helix chain 'C' and resid 34 through 40 Processing helix chain 'C' and resid 42 through 52 Processing helix chain 'C' and resid 57 through 66 Processing helix chain 'C' and resid 71 through 84 removed outlier: 3.556A pdb=" N THR C 84 " --> pdb=" O ALA C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 98 No H-bonds generated for 'chain 'C' and resid 96 through 98' Processing helix chain 'C' and resid 131 through 134 Processing helix chain 'C' and resid 155 through 161 Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 201 through 212 Processing helix chain 'C' and resid 282 through 299 removed outlier: 4.022A pdb=" N ALA C 296 " --> pdb=" O ARG C 292 " (cutoff:3.500A) Proline residue: C 297 - end of helix Processing helix chain 'C' and resid 306 through 308 No H-bonds generated for 'chain 'C' and resid 306 through 308' Processing helix chain 'C' and resid 310 through 315 Processing helix chain 'C' and resid 319 through 330 removed outlier: 4.027A pdb=" N LEU C 329 " --> pdb=" O PHE C 325 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS C 330 " --> pdb=" O VAL C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 352 Processing helix chain 'D' and resid 14 through 29 Processing helix chain 'D' and resid 50 through 59 Processing helix chain 'D' and resid 77 through 90 Processing helix chain 'D' and resid 138 through 146 removed outlier: 4.020A pdb=" N THR D 143 " --> pdb=" O THR D 139 " (cutoff:3.500A) Processing helix chain 'D' and resid 151 through 164 Processing helix chain 'D' and resid 190 through 196 Proline residue: D 194 - end of helix No H-bonds generated for 'chain 'D' and resid 190 through 196' Processing helix chain 'D' and resid 269 through 278 Processing helix chain 'E' and resid 4 through 17 Processing helix chain 'E' and resid 20 through 30 Processing helix chain 'E' and resid 53 through 55 No H-bonds generated for 'chain 'E' and resid 53 through 55' Processing helix chain 'E' and resid 89 through 102 Processing helix chain 'E' and resid 105 through 114 removed outlier: 4.422A pdb=" N GLN E 109 " --> pdb=" O SER E 105 " (cutoff:3.500A) removed outlier: 4.982A pdb=" N ASN E 110 " --> pdb=" O ARG E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 116 through 137 removed outlier: 3.683A pdb=" N ALA E 136 " --> pdb=" O ALA E 132 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N SER E 137 " --> pdb=" O GLU E 133 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 26 Processing helix chain 'F' and resid 46 through 55 Processing helix chain 'F' and resid 66 through 68 No H-bonds generated for 'chain 'F' and resid 66 through 68' Processing helix chain 'F' and resid 71 through 80 Processing helix chain 'F' and resid 89 through 91 No H-bonds generated for 'chain 'F' and resid 89 through 91' Processing helix chain 'F' and resid 103 through 108 Processing helix chain 'F' and resid 155 through 163 Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 34 through 40 Processing helix chain 'G' and resid 42 through 52 Processing helix chain 'G' and resid 57 through 66 Processing helix chain 'G' and resid 71 through 84 removed outlier: 3.556A pdb=" N THR G 84 " --> pdb=" O ALA G 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 98 No H-bonds generated for 'chain 'G' and resid 96 through 98' Processing helix chain 'G' and resid 131 through 134 Processing helix chain 'G' and resid 155 through 161 Processing helix chain 'G' and resid 189 through 197 Processing helix chain 'G' and resid 201 through 212 Processing helix chain 'G' and resid 282 through 299 removed outlier: 4.021A pdb=" N ALA G 296 " --> pdb=" O ARG G 292 " (cutoff:3.500A) Proline residue: G 297 - end of helix Processing helix chain 'G' and resid 306 through 308 No H-bonds generated for 'chain 'G' and resid 306 through 308' Processing helix chain 'G' and resid 310 through 315 Processing helix chain 'G' and resid 319 through 330 removed outlier: 4.027A pdb=" N LEU G 329 " --> pdb=" O PHE G 325 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N LYS G 330 " --> pdb=" O VAL G 326 " (cutoff:3.500A) Processing helix chain 'G' and resid 334 through 352 Processing helix chain 'H' and resid 14 through 29 Processing helix chain 'H' and resid 50 through 59 Processing helix chain 'H' and resid 77 through 90 Processing helix chain 'H' and resid 138 through 146 removed outlier: 4.019A pdb=" N THR H 143 " --> pdb=" O THR H 139 " (cutoff:3.500A) Processing helix chain 'H' and resid 151 through 164 Processing helix chain 'H' and resid 190 through 196 Proline residue: H 194 - end of helix No H-bonds generated for 'chain 'H' and resid 190 through 196' Processing helix chain 'H' and resid 269 through 278 Processing helix chain 'I' and resid 44 through 51 Processing helix chain 'I' and resid 74 through 83 Processing helix chain 'I' and resid 92 through 95 Processing helix chain 'I' and resid 102 through 113 removed outlier: 4.392A pdb=" N ARG I 109 " --> pdb=" O ASN I 105 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU I 110 " --> pdb=" O ILE I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 131 Processing helix chain 'I' and resid 136 through 138 No H-bonds generated for 'chain 'I' and resid 136 through 138' Processing helix chain 'I' and resid 143 through 145 No H-bonds generated for 'chain 'I' and resid 143 through 145' Processing helix chain 'I' and resid 148 through 160 Processing helix chain 'I' and resid 178 through 195 Processing helix chain 'I' and resid 206 through 212 Processing helix chain 'I' and resid 230 through 235 Processing helix chain 'I' and resid 240 through 247 Processing helix chain 'J' and resid 44 through 51 Processing helix chain 'J' and resid 74 through 83 Processing helix chain 'J' and resid 92 through 95 Processing helix chain 'J' and resid 102 through 113 removed outlier: 4.393A pdb=" N ARG J 109 " --> pdb=" O ASN J 105 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LEU J 110 " --> pdb=" O ILE J 106 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 131 Processing helix chain 'J' and resid 136 through 138 No H-bonds generated for 'chain 'J' and resid 136 through 138' Processing helix chain 'J' and resid 143 through 145 No H-bonds generated for 'chain 'J' and resid 143 through 145' Processing helix chain 'J' and resid 148 through 160 Processing helix chain 'J' and resid 178 through 195 Processing helix chain 'J' and resid 206 through 212 Processing helix chain 'J' and resid 230 through 235 Processing helix chain 'J' and resid 240 through 247 Processing helix chain 'K' and resid 47 through 54 Processing helix chain 'K' and resid 81 through 90 Processing helix chain 'K' and resid 107 through 118 Proline residue: K 114 - end of helix removed outlier: 4.111A pdb=" N THR K 118 " --> pdb=" O PRO K 114 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 135 Processing helix chain 'K' and resid 140 through 142 No H-bonds generated for 'chain 'K' and resid 140 through 142' Processing helix chain 'K' and resid 147 through 149 No H-bonds generated for 'chain 'K' and resid 147 through 149' Processing helix chain 'K' and resid 152 through 163 Processing helix chain 'K' and resid 182 through 198 Processing helix chain 'K' and resid 209 through 215 Processing helix chain 'L' and resid 47 through 54 Processing helix chain 'L' and resid 81 through 90 Processing helix chain 'L' and resid 107 through 118 Proline residue: L 114 - end of helix removed outlier: 4.110A pdb=" N THR L 118 " --> pdb=" O PRO L 114 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 135 Processing helix chain 'L' and resid 140 through 142 No H-bonds generated for 'chain 'L' and resid 140 through 142' Processing helix chain 'L' and resid 147 through 149 No H-bonds generated for 'chain 'L' and resid 147 through 149' Processing helix chain 'L' and resid 152 through 163 Processing helix chain 'L' and resid 182 through 198 Processing helix chain 'L' and resid 209 through 215 Processing sheet with id= A, first strand: chain 'A' and resid 43 through 48 Processing sheet with id= B, first strand: chain 'A' and resid 50 through 52 Processing sheet with id= C, first strand: chain 'A' and resid 36 through 40 removed outlier: 6.604A pdb=" N ALA A 71 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 62 through 64 removed outlier: 6.705A pdb=" N PHE B 94 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR B 122 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR B 97 " --> pdb=" O THR B 122 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE B 124 " --> pdb=" O THR B 97 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP B 173 " --> pdb=" O LEU B 123 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N LEU B 125 " --> pdb=" O ASP B 173 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE B 175 " --> pdb=" O LEU B 125 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 147 through 149 Processing sheet with id= F, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.631A pdb=" N SER C 227 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ARG C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE C 225 " --> pdb=" O ARG C 104 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU C 254 " --> pdb=" O GLY C 223 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 225 " --> pdb=" O GLU C 252 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU C 252 " --> pdb=" O ILE C 225 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N SER C 227 " --> pdb=" O MET C 250 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N MET C 250 " --> pdb=" O SER C 227 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR C 229 " --> pdb=" O LEU C 248 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU C 248 " --> pdb=" O TYR C 229 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP C 231 " --> pdb=" O GLY C 246 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N GLY C 246 " --> pdb=" O ASP C 231 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE C 259 " --> pdb=" O HIS C 268 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N HIS C 268 " --> pdb=" O PHE C 259 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'D' and resid 66 through 70 removed outlier: 6.421A pdb=" N LEU D 103 " --> pdb=" O LYS D 67 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE D 69 " --> pdb=" O LEU D 103 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N GLN D 105 " --> pdb=" O ILE D 69 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE D 120 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N THR D 106 " --> pdb=" O ILE D 120 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE D 122 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N LEU D 202 " --> pdb=" O ILE D 121 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE D 123 " --> pdb=" O LEU D 202 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LEU D 204 " --> pdb=" O PHE D 123 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 181 through 183 Processing sheet with id= I, first strand: chain 'D' and resid 251 through 255 Processing sheet with id= J, first strand: chain 'E' and resid 43 through 48 Processing sheet with id= K, first strand: chain 'E' and resid 50 through 52 Processing sheet with id= L, first strand: chain 'E' and resid 36 through 40 removed outlier: 6.603A pdb=" N ALA E 71 " --> pdb=" O ILE E 39 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'F' and resid 62 through 64 removed outlier: 6.705A pdb=" N PHE F 94 " --> pdb=" O TRP F 63 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N THR F 122 " --> pdb=" O ALA F 95 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N THR F 97 " --> pdb=" O THR F 122 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE F 124 " --> pdb=" O THR F 97 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N ASP F 173 " --> pdb=" O LEU F 123 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N LEU F 125 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N ILE F 175 " --> pdb=" O LEU F 125 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'F' and resid 147 through 149 Processing sheet with id= O, first strand: chain 'G' and resid 100 through 105 removed outlier: 6.632A pdb=" N SER G 227 " --> pdb=" O GLU G 102 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ARG G 104 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ILE G 225 " --> pdb=" O ARG G 104 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLU G 254 " --> pdb=" O GLY G 223 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE G 225 " --> pdb=" O GLU G 252 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N GLU G 252 " --> pdb=" O ILE G 225 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N SER G 227 " --> pdb=" O MET G 250 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET G 250 " --> pdb=" O SER G 227 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N TYR G 229 " --> pdb=" O LEU G 248 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LEU G 248 " --> pdb=" O TYR G 229 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ASP G 231 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLY G 246 " --> pdb=" O ASP G 231 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N PHE G 259 " --> pdb=" O HIS G 268 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N HIS G 268 " --> pdb=" O PHE G 259 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'H' and resid 66 through 70 removed outlier: 6.421A pdb=" N LEU H 103 " --> pdb=" O LYS H 67 " (cutoff:3.500A) removed outlier: 7.819A pdb=" N ILE H 69 " --> pdb=" O LEU H 103 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLN H 105 " --> pdb=" O ILE H 69 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N ILE H 120 " --> pdb=" O ILE H 104 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N THR H 106 " --> pdb=" O ILE H 120 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE H 122 " --> pdb=" O THR H 106 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU H 202 " --> pdb=" O ILE H 121 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N PHE H 123 " --> pdb=" O LEU H 202 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU H 204 " --> pdb=" O PHE H 123 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'H' and resid 181 through 183 Processing sheet with id= R, first strand: chain 'H' and resid 251 through 255 Processing sheet with id= S, first strand: chain 'I' and resid 26 through 28 Processing sheet with id= T, first strand: chain 'I' and resid 223 through 229 removed outlier: 6.974A pdb=" N VAL I 218 " --> pdb=" O VAL I 225 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER I 227 " --> pdb=" O LEU I 216 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU I 216 " --> pdb=" O SER I 227 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N VAL I 199 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE I 36 " --> pdb=" O VAL I 199 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE I 201 " --> pdb=" O ILE I 36 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLY I 38 " --> pdb=" O ILE I 201 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'I' and resid 13 through 16 removed outlier: 6.791A pdb=" N LYS I 19 " --> pdb=" O TYR I 15 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'J' and resid 26 through 28 Processing sheet with id= W, first strand: chain 'J' and resid 223 through 229 removed outlier: 6.974A pdb=" N VAL J 218 " --> pdb=" O VAL J 225 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N SER J 227 " --> pdb=" O LEU J 216 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LEU J 216 " --> pdb=" O SER J 227 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL J 199 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE J 36 " --> pdb=" O VAL J 199 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N ILE J 201 " --> pdb=" O ILE J 36 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N GLY J 38 " --> pdb=" O ILE J 201 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'J' and resid 13 through 16 removed outlier: 6.791A pdb=" N LYS J 19 " --> pdb=" O TYR J 15 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'K' and resid 29 through 31 Processing sheet with id= Z, first strand: chain 'K' and resid 218 through 221 removed outlier: 6.455A pdb=" N ILE K 202 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N LEU K 39 " --> pdb=" O ILE K 202 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N GLY K 204 " --> pdb=" O LEU K 39 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'K' and resid 9 through 13 removed outlier: 6.174A pdb=" N PHE K 11 " --> pdb=" O PRO K 22 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N LEU K 13 " --> pdb=" O ARG K 20 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ARG K 20 " --> pdb=" O LEU K 13 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'L' and resid 29 through 31 Processing sheet with id= AC, first strand: chain 'L' and resid 218 through 221 removed outlier: 6.456A pdb=" N ILE L 202 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N LEU L 39 " --> pdb=" O ILE L 202 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLY L 204 " --> pdb=" O LEU L 39 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'L' and resid 9 through 13 removed outlier: 6.173A pdb=" N PHE L 11 " --> pdb=" O PRO L 22 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU L 13 " --> pdb=" O ARG L 20 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ARG L 20 " --> pdb=" O LEU L 13 " (cutoff:3.500A) 864 hydrogen bonds defined for protein. 2454 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 18.53 Time building geometry restraints manager: 40.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 22224 1.02 - 1.22: 20 1.22 - 1.42: 9295 1.42 - 1.62: 13391 1.62 - 1.81: 182 Bond restraints: 45112 Sorted by residual: bond pdb=" C2' ANP I1002 " pdb=" C3' ANP I1002 " ideal model delta sigma weight residual 1.520 1.225 0.295 2.00e-02 2.50e+03 2.18e+02 bond pdb=" C2' ANP J1002 " pdb=" C3' ANP J1002 " ideal model delta sigma weight residual 1.520 1.225 0.295 2.00e-02 2.50e+03 2.17e+02 bond pdb=" C3' ANP I1002 " pdb=" O3' ANP I1002 " ideal model delta sigma weight residual 1.386 1.566 -0.180 2.00e-02 2.50e+03 8.11e+01 bond pdb=" C3' ANP J1002 " pdb=" O3' ANP J1002 " ideal model delta sigma weight residual 1.386 1.566 -0.180 2.00e-02 2.50e+03 8.10e+01 bond pdb=" C1' ANP I1002 " pdb=" C2' ANP I1002 " ideal model delta sigma weight residual 1.542 1.679 -0.137 2.00e-02 2.50e+03 4.71e+01 ... (remaining 45107 not shown) Histogram of bond angle deviations from ideal: 72.50 - 87.79: 27 87.79 - 103.08: 179 103.08 - 118.38: 61413 118.38 - 133.67: 19900 133.67 - 148.97: 29 Bond angle restraints: 81548 Sorted by residual: angle pdb=" N THR F 2 " pdb=" CA THR F 2 " pdb=" HA THR F 2 " ideal model delta sigma weight residual 110.00 73.48 36.52 3.00e+00 1.11e-01 1.48e+02 angle pdb=" C ALA A 3 " pdb=" CA ALA A 3 " pdb=" HA ALA A 3 " ideal model delta sigma weight residual 109.00 72.50 36.50 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N ALA A 3 " pdb=" CA ALA A 3 " pdb=" HA ALA A 3 " ideal model delta sigma weight residual 110.00 73.52 36.48 3.00e+00 1.11e-01 1.48e+02 angle pdb=" N ASP A 4 " pdb=" CA ASP A 4 " pdb=" HA ASP A 4 " ideal model delta sigma weight residual 110.00 73.57 36.43 3.00e+00 1.11e-01 1.47e+02 angle pdb=" CB ASP A 4 " pdb=" CA ASP A 4 " pdb=" HA ASP A 4 " ideal model delta sigma weight residual 109.00 72.84 36.16 3.00e+00 1.11e-01 1.45e+02 ... (remaining 81543 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 19400 17.84 - 35.68: 1140 35.68 - 53.52: 473 53.52 - 71.36: 145 71.36 - 89.20: 66 Dihedral angle restraints: 21224 sinusoidal: 11818 harmonic: 9406 Sorted by residual: dihedral pdb=" CA ARG G 100 " pdb=" C ARG G 100 " pdb=" N LEU G 101 " pdb=" CA LEU G 101 " ideal model delta harmonic sigma weight residual -180.00 -159.61 -20.39 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ARG C 100 " pdb=" C ARG C 100 " pdb=" N LEU C 101 " pdb=" CA LEU C 101 " ideal model delta harmonic sigma weight residual -180.00 -159.65 -20.35 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA LEU B 130 " pdb=" C LEU B 130 " pdb=" N SER B 131 " pdb=" CA SER B 131 " ideal model delta harmonic sigma weight residual -180.00 -162.26 -17.74 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 21221 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 3393 0.104 - 0.208: 148 0.208 - 0.312: 11 0.312 - 0.416: 0 0.416 - 0.521: 4 Chirality restraints: 3556 Sorted by residual: chirality pdb=" CB THR F 5 " pdb=" CA THR F 5 " pdb=" OG1 THR F 5 " pdb=" CG2 THR F 5 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.78e+00 chirality pdb=" CB THR B 5 " pdb=" CA THR B 5 " pdb=" OG1 THR B 5 " pdb=" CG2 THR B 5 " both_signs ideal model delta sigma weight residual False 2.55 2.03 0.52 2.00e-01 2.50e+01 6.69e+00 chirality pdb=" CB THR F 2 " pdb=" CA THR F 2 " pdb=" OG1 THR F 2 " pdb=" CG2 THR F 2 " both_signs ideal model delta sigma weight residual False 2.55 2.08 0.48 2.00e-01 2.50e+01 5.65e+00 ... (remaining 3553 not shown) Planarity restraints: 6800 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 98 " -0.043 2.00e-02 2.50e+03 4.07e-02 4.96e+01 pdb=" CG PHE L 98 " 0.080 2.00e-02 2.50e+03 pdb=" CD1 PHE L 98 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE L 98 " -0.071 2.00e-02 2.50e+03 pdb=" CE1 PHE L 98 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE L 98 " -0.029 2.00e-02 2.50e+03 pdb=" CZ PHE L 98 " -0.007 2.00e-02 2.50e+03 pdb=" HD1 PHE L 98 " 0.021 2.00e-02 2.50e+03 pdb=" HD2 PHE L 98 " 0.058 2.00e-02 2.50e+03 pdb=" HE1 PHE L 98 " -0.013 2.00e-02 2.50e+03 pdb=" HE2 PHE L 98 " -0.006 2.00e-02 2.50e+03 pdb=" HZ PHE L 98 " 0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 98 " 0.030 2.00e-02 2.50e+03 3.63e-02 3.95e+01 pdb=" CG PHE K 98 " -0.100 2.00e-02 2.50e+03 pdb=" CD1 PHE K 98 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE K 98 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 PHE K 98 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE K 98 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE K 98 " -0.025 2.00e-02 2.50e+03 pdb=" HD1 PHE K 98 " 0.024 2.00e-02 2.50e+03 pdb=" HD2 PHE K 98 " 0.015 2.00e-02 2.50e+03 pdb=" HE1 PHE K 98 " 0.022 2.00e-02 2.50e+03 pdb=" HE2 PHE K 98 " -0.009 2.00e-02 2.50e+03 pdb=" HZ PHE K 98 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN K 156 " -0.016 2.00e-02 2.50e+03 4.56e-02 3.12e+01 pdb=" CD GLN K 156 " 0.080 2.00e-02 2.50e+03 pdb=" OE1 GLN K 156 " -0.047 2.00e-02 2.50e+03 pdb=" NE2 GLN K 156 " 0.039 2.00e-02 2.50e+03 pdb="HE21 GLN K 156 " -0.045 2.00e-02 2.50e+03 pdb="HE22 GLN K 156 " -0.010 2.00e-02 2.50e+03 ... (remaining 6797 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.09: 1084 2.09 - 2.72: 76981 2.72 - 3.34: 139891 3.34 - 3.97: 183794 3.97 - 4.60: 284382 Nonbonded interactions: 686132 Sorted by model distance: nonbonded pdb=" OE2 GLU A 58 " pdb=" H SER C 171 " model vdw 1.460 1.850 nonbonded pdb=" OE2 GLU E 58 " pdb=" H SER G 171 " model vdw 1.463 1.850 nonbonded pdb=" OE2 GLU A 37 " pdb="HH11 ARG A 73 " model vdw 1.509 1.850 nonbonded pdb=" OE2 GLU E 37 " pdb="HH11 ARG E 73 " model vdw 1.518 1.850 nonbonded pdb=" OD1 ASP G 95 " pdb=" HG1 THR G 97 " model vdw 1.570 1.850 ... (remaining 686127 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.020 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: 0.610 Extract box with map and model: 17.640 Check model and map are aligned: 0.720 Set scattering table: 0.410 Process input model: 151.970 Find NCS groups from input model: 1.930 Set up NCS constraints: 0.290 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: 0.020 Load rotamer database and sin/cos tables:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 189.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.295 22872 Z= 0.365 Angle : 0.726 27.099 31096 Z= 0.353 Chirality : 0.048 0.521 3556 Planarity : 0.005 0.090 4086 Dihedral : 14.766 89.199 8542 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.04 % Allowed : 6.89 % Favored : 92.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.45 (0.16), residues: 2858 helix: 1.82 (0.16), residues: 1134 sheet: 0.26 (0.23), residues: 490 loop : 0.61 (0.18), residues: 1234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 11 HIS 0.015 0.001 HIS L 144 PHE 0.094 0.002 PHE K 98 TYR 0.034 0.002 TYR L 58 ARG 0.022 0.001 ARG L 52 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 444 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 419 time to evaluate : 3.611 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: C 287 MET cc_start: 0.8659 (ttt) cc_final: 0.8280 (ttt) REVERT: H 153 MET cc_start: 0.8396 (tpp) cc_final: 0.8190 (tpp) REVERT: K 74 VAL cc_start: 0.8610 (OUTLIER) cc_final: 0.8387 (t) REVERT: L 74 VAL cc_start: 0.8580 (OUTLIER) cc_final: 0.8356 (t) REVERT: L 144 HIS cc_start: 0.7724 (m-70) cc_final: 0.7522 (m-70) outliers start: 25 outliers final: 8 residues processed: 433 average time/residue: 2.8387 time to fit residues: 1413.5879 Evaluate side-chains 327 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 317 time to evaluate : 3.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 242 THR Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 242 THR Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 2.9990 chunk 215 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 145 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 135 optimal weight: 0.9990 chunk 165 optimal weight: 2.9990 chunk 257 optimal weight: 1.9990 overall best weight: 1.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN B 107 ASN C 353 HIS D 34 GLN E 19 GLN E 28 ASN E 90 GLN F 107 ASN G 353 HIS H 34 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 22872 Z= 0.219 Angle : 0.533 11.393 31096 Z= 0.269 Chirality : 0.053 1.368 3556 Planarity : 0.004 0.053 4086 Dihedral : 6.498 49.124 3222 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.21 % Allowed : 9.31 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.55 (0.16), residues: 2858 helix: 1.82 (0.16), residues: 1152 sheet: 0.40 (0.23), residues: 496 loop : 0.70 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 11 HIS 0.004 0.001 HIS G 353 PHE 0.013 0.001 PHE B 18 TYR 0.019 0.002 TYR I 241 ARG 0.005 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 353 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 324 time to evaluate : 2.905 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: C 166 LYS cc_start: 0.8789 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: C 287 MET cc_start: 0.8720 (ttt) cc_final: 0.8374 (ttt) REVERT: G 166 LYS cc_start: 0.8790 (OUTLIER) cc_final: 0.8563 (mtmm) REVERT: G 287 MET cc_start: 0.8708 (ttt) cc_final: 0.8373 (ttt) REVERT: I 111 MET cc_start: 0.8743 (mtm) cc_final: 0.8446 (mtm) REVERT: K 74 VAL cc_start: 0.8610 (t) cc_final: 0.8303 (t) REVERT: K 219 LEU cc_start: 0.8223 (OUTLIER) cc_final: 0.8002 (tp) REVERT: L 74 VAL cc_start: 0.8557 (t) cc_final: 0.8317 (t) outliers start: 29 outliers final: 11 residues processed: 341 average time/residue: 2.9934 time to fit residues: 1166.2903 Evaluate side-chains 324 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 310 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 141 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 141 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 179 SER Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 45 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 143 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 214 optimal weight: 4.9990 chunk 175 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 258 optimal weight: 0.8980 chunk 279 optimal weight: 3.9990 chunk 230 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 overall best weight: 0.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN B 107 ASN C 149 GLN C 353 HIS E 19 GLN E 90 GLN G 149 GLN G 353 HIS L 156 GLN L 159 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22872 Z= 0.183 Angle : 0.499 10.948 31096 Z= 0.255 Chirality : 0.053 1.342 3556 Planarity : 0.004 0.038 4086 Dihedral : 5.626 48.935 3216 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 1.00 % Allowed : 9.90 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.70 (0.16), residues: 2858 helix: 1.99 (0.16), residues: 1152 sheet: 0.39 (0.23), residues: 494 loop : 0.78 (0.18), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 11 HIS 0.004 0.001 HIS G 353 PHE 0.013 0.001 PHE B 18 TYR 0.015 0.001 TYR I 241 ARG 0.002 0.000 ARG L 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 339 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 315 time to evaluate : 3.538 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: C 166 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8572 (mtmm) REVERT: C 287 MET cc_start: 0.8736 (ttt) cc_final: 0.8402 (ttt) REVERT: G 166 LYS cc_start: 0.8775 (OUTLIER) cc_final: 0.8564 (mtmm) REVERT: I 111 MET cc_start: 0.8738 (mtm) cc_final: 0.8492 (mtm) REVERT: K 74 VAL cc_start: 0.8637 (OUTLIER) cc_final: 0.8360 (t) REVERT: L 10 THR cc_start: 0.7136 (p) cc_final: 0.6642 (t) REVERT: L 74 VAL cc_start: 0.8644 (t) cc_final: 0.8331 (t) outliers start: 24 outliers final: 7 residues processed: 325 average time/residue: 2.9571 time to fit residues: 1098.8800 Evaluate side-chains 301 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 291 time to evaluate : 3.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 166 LYS Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 166 LYS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 74 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 255 optimal weight: 2.9990 chunk 194 optimal weight: 3.9990 chunk 134 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 123 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 259 optimal weight: 6.9990 chunk 274 optimal weight: 0.1980 chunk 135 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 28 ASN A 90 GLN C 149 GLN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 90 GLN E 131 GLN G 149 GLN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 GLN K 159 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 22872 Z= 0.300 Angle : 0.540 10.998 31096 Z= 0.280 Chirality : 0.054 1.369 3556 Planarity : 0.004 0.038 4086 Dihedral : 5.514 52.157 3214 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.92 % Allowed : 10.53 % Favored : 88.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.56 (0.16), residues: 2858 helix: 1.83 (0.16), residues: 1148 sheet: 0.34 (0.23), residues: 490 loop : 0.74 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 11 HIS 0.005 0.001 HIS G 316 PHE 0.016 0.002 PHE B 18 TYR 0.014 0.002 TYR I 241 ARG 0.004 0.001 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 311 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 289 time to evaluate : 3.858 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: C 287 MET cc_start: 0.8701 (ttt) cc_final: 0.8320 (ttt) REVERT: F 8 MET cc_start: 0.6714 (mmt) cc_final: 0.6508 (mmp) REVERT: G 287 MET cc_start: 0.8699 (ttt) cc_final: 0.8329 (ttt) REVERT: I 189 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8243 (mmp-170) REVERT: J 61 GLU cc_start: 0.7105 (OUTLIER) cc_final: 0.6253 (mp0) REVERT: J 189 ARG cc_start: 0.8484 (OUTLIER) cc_final: 0.8253 (mmp-170) REVERT: K 10 THR cc_start: 0.7218 (p) cc_final: 0.6713 (t) REVERT: K 74 VAL cc_start: 0.8604 (OUTLIER) cc_final: 0.8320 (t) REVERT: K 89 LYS cc_start: 0.8267 (ttmt) cc_final: 0.8018 (tppt) REVERT: K 156 GLN cc_start: 0.7376 (tp40) cc_final: 0.7158 (tp-100) REVERT: K 219 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.8047 (tp) REVERT: L 10 THR cc_start: 0.7244 (p) cc_final: 0.6747 (t) REVERT: L 74 VAL cc_start: 0.8602 (OUTLIER) cc_final: 0.8327 (t) outliers start: 22 outliers final: 9 residues processed: 304 average time/residue: 2.9773 time to fit residues: 1038.5377 Evaluate side-chains 297 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 282 time to evaluate : 3.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain K residue 219 LEU Chi-restraints excluded: chain L residue 45 SER Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 219 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 228 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 204 optimal weight: 0.4980 chunk 113 optimal weight: 1.9990 chunk 234 optimal weight: 0.8980 chunk 189 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 140 optimal weight: 2.9990 chunk 246 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 150 GLN E 19 GLN E 90 GLN G 149 GLN J 223 GLN K 159 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22872 Z= 0.211 Angle : 0.508 11.159 31096 Z= 0.262 Chirality : 0.054 1.389 3556 Planarity : 0.004 0.037 4086 Dihedral : 5.304 48.552 3214 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 2.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.67 % Allowed : 10.94 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.61 (0.16), residues: 2858 helix: 1.93 (0.16), residues: 1148 sheet: 0.28 (0.23), residues: 488 loop : 0.74 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 11 HIS 0.004 0.001 HIS G 353 PHE 0.013 0.001 PHE F 18 TYR 0.014 0.001 TYR J 241 ARG 0.003 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 306 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 290 time to evaluate : 3.355 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: B 8 MET cc_start: 0.6661 (mmt) cc_final: 0.6425 (mmp) REVERT: C 287 MET cc_start: 0.8709 (ttt) cc_final: 0.8297 (ttt) REVERT: F 8 MET cc_start: 0.6704 (mmt) cc_final: 0.6456 (mmp) REVERT: G 287 MET cc_start: 0.8711 (ttt) cc_final: 0.8324 (ttt) REVERT: H 196 MET cc_start: 0.8633 (mtp) cc_final: 0.8396 (mtp) REVERT: I 61 GLU cc_start: 0.7083 (OUTLIER) cc_final: 0.6229 (mp0) REVERT: I 189 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.8202 (mmp-170) REVERT: J 189 ARG cc_start: 0.8442 (OUTLIER) cc_final: 0.8186 (mmp-170) REVERT: K 10 THR cc_start: 0.7285 (p) cc_final: 0.6785 (t) REVERT: K 74 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8315 (t) REVERT: K 89 LYS cc_start: 0.8259 (ttmt) cc_final: 0.8016 (tppt) REVERT: K 140 GLU cc_start: 0.7718 (tm-30) cc_final: 0.7499 (tm-30) REVERT: K 156 GLN cc_start: 0.7411 (tp40) cc_final: 0.7186 (tp-100) REVERT: L 10 THR cc_start: 0.7243 (p) cc_final: 0.6747 (t) REVERT: L 74 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8315 (t) REVERT: L 109 GLU cc_start: 0.8187 (mp0) cc_final: 0.7691 (mp0) outliers start: 16 outliers final: 8 residues processed: 299 average time/residue: 3.0209 time to fit residues: 1034.3985 Evaluate side-chains 295 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 282 time to evaluate : 3.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 27 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 27 THR Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 219 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 92 optimal weight: 0.5980 chunk 247 optimal weight: 5.9990 chunk 54 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 67 optimal weight: 0.7980 chunk 274 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 144 optimal weight: 1.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 150 GLN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 90 GLN G 149 GLN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22872 Z= 0.224 Angle : 0.507 11.149 31096 Z= 0.262 Chirality : 0.054 1.384 3556 Planarity : 0.004 0.036 4086 Dihedral : 5.237 50.335 3214 Min Nonbonded Distance : 1.860 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.92 % Allowed : 10.65 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.60 (0.16), residues: 2858 helix: 1.93 (0.16), residues: 1148 sheet: 0.22 (0.23), residues: 488 loop : 0.75 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 11 HIS 0.004 0.001 HIS C 353 PHE 0.014 0.001 PHE B 18 TYR 0.013 0.001 TYR J 241 ARG 0.003 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 300 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 278 time to evaluate : 3.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 287 MET cc_start: 0.8719 (ttt) cc_final: 0.8297 (ttt) REVERT: E 124 MET cc_start: 0.7759 (mmp) cc_final: 0.7532 (mmp) REVERT: G 287 MET cc_start: 0.8717 (ttt) cc_final: 0.8312 (ttt) REVERT: I 61 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6239 (mp0) REVERT: I 189 ARG cc_start: 0.8465 (OUTLIER) cc_final: 0.8208 (mmp-170) REVERT: I 251 GLN cc_start: 0.7096 (mm-40) cc_final: 0.6891 (mm-40) REVERT: J 61 GLU cc_start: 0.7086 (OUTLIER) cc_final: 0.6221 (mp0) REVERT: J 189 ARG cc_start: 0.8444 (OUTLIER) cc_final: 0.8188 (mmp-170) REVERT: K 10 THR cc_start: 0.7296 (p) cc_final: 0.6805 (t) REVERT: K 74 VAL cc_start: 0.8578 (OUTLIER) cc_final: 0.8295 (t) REVERT: K 89 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7989 (tppt) REVERT: K 156 GLN cc_start: 0.7414 (tp40) cc_final: 0.7179 (tp-100) REVERT: L 10 THR cc_start: 0.7257 (p) cc_final: 0.6758 (t) REVERT: L 74 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8275 (t) REVERT: L 109 GLU cc_start: 0.8238 (mp0) cc_final: 0.7675 (mp0) outliers start: 22 outliers final: 7 residues processed: 287 average time/residue: 2.9656 time to fit residues: 973.8496 Evaluate side-chains 285 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 272 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 127 LYS Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 127 LYS Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 74 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 264 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 231 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 273 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 166 optimal weight: 0.8980 chunk 126 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 149 GLN C 150 GLN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 90 GLN G 149 GLN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 22872 Z= 0.248 Angle : 0.517 11.161 31096 Z= 0.268 Chirality : 0.054 1.391 3556 Planarity : 0.004 0.037 4086 Dihedral : 5.320 51.859 3214 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.75 % Allowed : 10.94 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.52 (0.16), residues: 2858 helix: 1.86 (0.16), residues: 1148 sheet: 0.18 (0.23), residues: 488 loop : 0.71 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 11 HIS 0.004 0.001 HIS G 316 PHE 0.014 0.002 PHE B 18 TYR 0.014 0.001 TYR J 241 ARG 0.003 0.000 ARG J 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 293 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 275 time to evaluate : 3.543 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: C 287 MET cc_start: 0.8695 (ttt) cc_final: 0.8290 (ttt) REVERT: E 124 MET cc_start: 0.7762 (mmp) cc_final: 0.7542 (mmt) REVERT: G 287 MET cc_start: 0.8705 (ttt) cc_final: 0.8299 (ttt) REVERT: I 61 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6234 (mp0) REVERT: I 111 MET cc_start: 0.8751 (mtm) cc_final: 0.8505 (mtm) REVERT: I 189 ARG cc_start: 0.8476 (OUTLIER) cc_final: 0.8219 (mmp-170) REVERT: J 189 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8224 (mmp-170) REVERT: K 10 THR cc_start: 0.7303 (p) cc_final: 0.6812 (t) REVERT: K 74 VAL cc_start: 0.8551 (t) cc_final: 0.8276 (t) REVERT: K 89 LYS cc_start: 0.8262 (ttmt) cc_final: 0.8021 (tppt) REVERT: K 156 GLN cc_start: 0.7410 (tp40) cc_final: 0.7179 (tp-100) REVERT: L 10 THR cc_start: 0.7271 (p) cc_final: 0.6769 (t) REVERT: L 74 VAL cc_start: 0.8513 (OUTLIER) cc_final: 0.8241 (t) outliers start: 18 outliers final: 8 residues processed: 285 average time/residue: 2.9693 time to fit residues: 968.2966 Evaluate side-chains 284 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 272 time to evaluate : 3.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 THR Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain K residue 45 SER Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 169 optimal weight: 0.0870 chunk 109 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 174 optimal weight: 0.9990 chunk 186 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 215 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 overall best weight: 1.2164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 150 GLN E 19 GLN E 90 GLN G 149 GLN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22872 Z= 0.208 Angle : 0.505 11.179 31096 Z= 0.261 Chirality : 0.054 1.390 3556 Planarity : 0.004 0.036 4086 Dihedral : 5.291 54.015 3214 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.71 % Allowed : 11.03 % Favored : 88.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.57 (0.16), residues: 2858 helix: 1.93 (0.16), residues: 1150 sheet: 0.19 (0.23), residues: 488 loop : 0.72 (0.18), residues: 1220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 11 HIS 0.004 0.001 HIS C 353 PHE 0.013 0.001 PHE B 18 TYR 0.011 0.001 TYR I 241 ARG 0.002 0.000 ARG A 59 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 295 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 278 time to evaluate : 3.420 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: C 287 MET cc_start: 0.8714 (ttt) cc_final: 0.8310 (ttt) REVERT: E 124 MET cc_start: 0.7761 (mmp) cc_final: 0.7546 (mmt) REVERT: G 287 MET cc_start: 0.8705 (ttt) cc_final: 0.8312 (ttt) REVERT: I 61 GLU cc_start: 0.7078 (OUTLIER) cc_final: 0.6210 (mp0) REVERT: I 111 MET cc_start: 0.8745 (mtm) cc_final: 0.8545 (mtm) REVERT: I 189 ARG cc_start: 0.8433 (OUTLIER) cc_final: 0.8145 (mmp-170) REVERT: J 61 GLU cc_start: 0.7068 (OUTLIER) cc_final: 0.6194 (mp0) REVERT: J 189 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8150 (mmp-170) REVERT: K 10 THR cc_start: 0.7297 (p) cc_final: 0.6785 (t) REVERT: K 74 VAL cc_start: 0.8525 (t) cc_final: 0.8248 (t) REVERT: K 89 LYS cc_start: 0.8261 (ttmt) cc_final: 0.8017 (tppt) REVERT: K 156 GLN cc_start: 0.7412 (tp40) cc_final: 0.7180 (tp-100) REVERT: L 10 THR cc_start: 0.7282 (p) cc_final: 0.6779 (t) REVERT: L 74 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8237 (t) outliers start: 17 outliers final: 6 residues processed: 288 average time/residue: 2.9752 time to fit residues: 983.0502 Evaluate side-chains 281 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 270 time to evaluate : 3.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 61 GLU Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 262 optimal weight: 9.9990 chunk 239 optimal weight: 2.9990 chunk 255 optimal weight: 4.9990 chunk 153 optimal weight: 2.9990 chunk 111 optimal weight: 1.9990 chunk 200 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 230 optimal weight: 1.9990 chunk 241 optimal weight: 6.9990 chunk 254 optimal weight: 0.9990 chunk 167 optimal weight: 0.2980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN C 150 GLN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 19 GLN E 90 GLN G 149 GLN K 32 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 22872 Z= 0.269 Angle : 0.528 11.153 31096 Z= 0.275 Chirality : 0.054 1.390 3556 Planarity : 0.004 0.052 4086 Dihedral : 5.410 54.413 3214 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.54 % Allowed : 11.57 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.46 (0.16), residues: 2858 helix: 1.79 (0.16), residues: 1148 sheet: 0.16 (0.23), residues: 488 loop : 0.69 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP E 11 HIS 0.004 0.001 HIS C 316 PHE 0.015 0.002 PHE F 18 TYR 0.012 0.002 TYR J 241 ARG 0.003 0.000 ARG J 122 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 284 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 271 time to evaluate : 3.511 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: C 287 MET cc_start: 0.8690 (ttt) cc_final: 0.8303 (ttt) REVERT: E 124 MET cc_start: 0.7770 (mmp) cc_final: 0.7561 (mmt) REVERT: G 287 MET cc_start: 0.8689 (ttt) cc_final: 0.8314 (ttt) REVERT: I 61 GLU cc_start: 0.7094 (OUTLIER) cc_final: 0.6232 (mp0) REVERT: I 111 MET cc_start: 0.8782 (mtm) cc_final: 0.8559 (mtm) REVERT: I 189 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8230 (mmp-170) REVERT: J 189 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8211 (mmp-170) REVERT: K 10 THR cc_start: 0.7309 (p) cc_final: 0.6808 (t) REVERT: K 74 VAL cc_start: 0.8514 (t) cc_final: 0.8230 (t) REVERT: K 89 LYS cc_start: 0.8279 (ttmt) cc_final: 0.8014 (ttmt) REVERT: K 156 GLN cc_start: 0.7436 (tp40) cc_final: 0.7196 (tp-100) REVERT: L 10 THR cc_start: 0.7287 (p) cc_final: 0.6780 (t) REVERT: L 74 VAL cc_start: 0.8499 (OUTLIER) cc_final: 0.8223 (t) outliers start: 13 outliers final: 8 residues processed: 278 average time/residue: 3.0189 time to fit residues: 958.5054 Evaluate side-chains 278 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 266 time to evaluate : 3.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Chi-restraints excluded: chain L residue 156 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 7.9990 chunk 164 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 187 optimal weight: 2.9990 chunk 282 optimal weight: 10.0000 chunk 260 optimal weight: 10.0000 chunk 225 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 174 optimal weight: 0.8980 chunk 138 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN C 150 GLN ** C 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 90 GLN G 149 GLN G 150 GLN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 22872 Z= 0.281 Angle : 0.533 11.153 31096 Z= 0.278 Chirality : 0.054 1.392 3556 Planarity : 0.004 0.038 4086 Dihedral : 5.478 56.915 3214 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 0.63 % Allowed : 11.45 % Favored : 87.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.40 (0.16), residues: 2858 helix: 1.73 (0.16), residues: 1148 sheet: 0.13 (0.23), residues: 488 loop : 0.67 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 11 HIS 0.004 0.001 HIS J 13 PHE 0.015 0.002 PHE F 18 TYR 0.012 0.002 TYR J 241 ARG 0.003 0.000 ARG I 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5716 Ramachandran restraints generated. 2858 Oldfield, 0 Emsley, 2858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue LEU 85 is missing expected H atoms. Skipping. Residue ALA 322 is missing expected H atoms. Skipping. Residue LYS 351 is missing expected H atoms. Skipping. Residue LEU 103 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Residue VAL 208 is missing expected H atoms. Skipping. Evaluate side-chains 286 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 271 time to evaluate : 3.464 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: C 287 MET cc_start: 0.8688 (ttt) cc_final: 0.8304 (ttt) REVERT: E 124 MET cc_start: 0.7777 (mmp) cc_final: 0.7566 (mmt) REVERT: G 287 MET cc_start: 0.8686 (ttt) cc_final: 0.8316 (ttt) REVERT: I 61 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6223 (mp0) REVERT: I 189 ARG cc_start: 0.8479 (OUTLIER) cc_final: 0.8206 (mmp-170) REVERT: J 189 ARG cc_start: 0.8480 (OUTLIER) cc_final: 0.8210 (mmp-170) REVERT: K 10 THR cc_start: 0.7314 (p) cc_final: 0.6814 (t) REVERT: K 74 VAL cc_start: 0.8505 (t) cc_final: 0.8235 (t) REVERT: K 89 LYS cc_start: 0.8294 (ttmt) cc_final: 0.8001 (ttmt) REVERT: L 10 THR cc_start: 0.7296 (p) cc_final: 0.6791 (t) REVERT: L 74 VAL cc_start: 0.8505 (OUTLIER) cc_final: 0.8242 (t) outliers start: 15 outliers final: 7 residues processed: 279 average time/residue: 3.1576 time to fit residues: 1002.9450 Evaluate side-chains 282 residues out of total 2396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 271 time to evaluate : 3.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain C residue 328 HIS Chi-restraints excluded: chain F residue 71 ASP Chi-restraints excluded: chain G residue 328 HIS Chi-restraints excluded: chain I residue 61 GLU Chi-restraints excluded: chain I residue 189 ARG Chi-restraints excluded: chain J residue 189 ARG Chi-restraints excluded: chain J residue 229 LEU Chi-restraints excluded: chain K residue 23 VAL Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 74 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 240 optimal weight: 9.9990 chunk 69 optimal weight: 1.9990 chunk 207 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 225 optimal weight: 3.9990 chunk 94 optimal weight: 0.4980 chunk 231 optimal weight: 0.9980 chunk 28 optimal weight: 0.0170 chunk 41 optimal weight: 2.9990 chunk 198 optimal weight: 3.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 GLN A 90 GLN A 131 GLN C 150 GLN E 19 GLN E 90 GLN G 149 GLN G 150 GLN ** G 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 5 GLN K 32 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.107851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.079012 restraints weight = 80830.501| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.58 r_work: 0.2918 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2835 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 22872 Z= 0.140 Angle : 0.492 11.279 31096 Z= 0.254 Chirality : 0.053 1.399 3556 Planarity : 0.004 0.036 4086 Dihedral : 5.242 58.204 3214 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.54 % Allowed : 11.57 % Favored : 87.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: 1.64 (0.16), residues: 2858 helix: 2.03 (0.16), residues: 1150 sheet: 0.17 (0.23), residues: 486 loop : 0.74 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP E 11 HIS 0.004 0.001 HIS C 353 PHE 0.010 0.001 PHE F 18 TYR 0.011 0.001 TYR I 241 ARG 0.005 0.000 ARG L 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17398.04 seconds wall clock time: 307 minutes 10.07 seconds (18430.07 seconds total)