Starting phenix.real_space_refine on Mon Nov 18 11:32:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es9_19940/11_2024/9es9_19940.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es9_19940/11_2024/9es9_19940.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.33 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es9_19940/11_2024/9es9_19940.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es9_19940/11_2024/9es9_19940.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es9_19940/11_2024/9es9_19940.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9es9_19940/11_2024/9es9_19940.cif" } resolution = 2.33 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= 0.001 sd= 0.034 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: 7 Type Number sf(0) Gaussians Fe 12 7.16 5 Br 4 7.06 5 Mg 2 5.21 5 S 72 5.16 5 C 10774 2.51 5 N 2530 2.21 5 O 3056 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16450 Number of models: 1 Model: "" Number of chains: 26 Chain: "A" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1697 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 203} Chain: "B" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 141} Chain: "C" Number of atoms: 2168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2168 Classifications: {'peptide': 279} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 255} Chain breaks: 1 Chain: "D" Number of atoms: 1334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1334 Classifications: {'peptide': 179} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 164} Chain: "E" Number of atoms: 243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 243 Classifications: {'peptide': 31} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 280 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} Conformer: "B" Number of residues, atoms: 37, 269 Classifications: {'peptide': 37} Link IDs: {'TRANS': 36} bond proxies already assigned to first conformer: 257 Chain: "G" Number of atoms: 261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 261 Classifications: {'peptide': 33} Link IDs: {'PTRANS': 1, 'TRANS': 31} Chain: "H" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 222 Classifications: {'peptide': 29} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 219 Classifications: {'peptide': 26} Link IDs: {'PTRANS': 1, 'TRANS': 24} Chain: "A" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 232 Unusual residues: {'BNT': 1, 'HEC': 1, 'HEM': 2, 'LMG': 1, 'UMQ': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 65 Unusual residues: {'CLA': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 58 Unusual residues: {'FES': 1, 'SQD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 74 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 74 Unusual residues: {'BCR': 1, 'UMQ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "B" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "C" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 29 Classifications: {'water': 29} Link IDs: {None: 28} Chain: "J" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "K" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 48 Classifications: {'water': 48} Link IDs: {None: 47} Chain: "L" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5869 SG CYS D 107 105.888 53.723 42.098 1.00 88.59 S ATOM 6005 SG CYS D 125 105.767 57.619 42.247 1.00 68.61 S Restraints were copied for chains: K, O, P, I, J, L, M, N, R Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N APHE F 7 " occ=0.60 ... (20 atoms not shown) pdb=" CZ BPHE F 7 " occ=0.40 residue: pdb=" N APHE N 7 " occ=0.60 ... (20 atoms not shown) pdb=" CZ BPHE N 7 " occ=0.40 Time building chain proxies: 11.56, per 1000 atoms: 0.70 Number of scatterers: 16450 At special positions: 0 Unit cell: (148.78, 116.1, 117.82, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 4 34.99 Fe 12 26.01 S 72 16.00 Mg 2 11.99 O 3056 8.00 N 2530 7.00 C 10774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 112 " - pdb=" SG CYS D 127 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 2.4 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES D 202 " pdb="FE1 FES D 202 " - pdb=" ND1 HIS D 109 " pdb="FE1 FES D 202 " - pdb=" ND1 HIS D 128 " pdb="FE2 FES D 202 " - pdb=" SG CYS D 107 " pdb="FE2 FES D 202 " - pdb=" SG CYS D 125 " pdb=" FES L 202 " pdb="FE1 FES L 202 " - pdb=" ND1 HIS L 109 " pdb="FE1 FES L 202 " - pdb=" ND1 HIS L 128 " pdb="FE2 FES L 202 " - pdb=" SG CYS L 125 " pdb="FE2 FES L 202 " - pdb=" SG CYS L 107 " Number of angles added : 6 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3604 Finding SS restraints... Secondary structure from input PDB file: 68 helices and 14 sheets defined 51.2% alpha, 9.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.084A pdb=" N ARG A 11 " --> pdb=" O TRP A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 22 Processing helix chain 'A' and resid 31 through 34 Processing helix chain 'A' and resid 35 through 55 removed outlier: 3.547A pdb=" N THR A 55 " --> pdb=" O GLY A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 75 Processing helix chain 'A' and resid 78 through 107 removed outlier: 3.588A pdb=" N ALA A 90 " --> pdb=" O HIS A 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A 91 " --> pdb=" O ARG A 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 137 removed outlier: 3.537A pdb=" N TRP A 118 " --> pdb=" O ARG A 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 removed outlier: 3.508A pdb=" N LYS A 149 " --> pdb=" O TYR A 145 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE A 150 " --> pdb=" O TRP A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 158 Processing helix chain 'A' and resid 161 through 171 removed outlier: 3.524A pdb=" N LEU A 168 " --> pdb=" O PRO A 164 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 189 Processing helix chain 'A' and resid 189 through 210 Processing helix chain 'B' and resid 11 through 20 removed outlier: 3.680A pdb=" N LYS B 20 " --> pdb=" O ALA B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 39 through 58 Processing helix chain 'B' and resid 78 through 80 No H-bonds generated for 'chain 'B' and resid 78 through 80' Processing helix chain 'B' and resid 81 through 91 removed outlier: 3.500A pdb=" N ARG B 89 " --> pdb=" O PHE B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.824A pdb=" N VAL B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Proline residue: B 105 - end of helix Processing helix chain 'B' and resid 122 through 125 Processing helix chain 'B' and resid 126 through 147 Processing helix chain 'B' and resid 148 through 149 No H-bonds generated for 'chain 'B' and resid 148 through 149' Processing helix chain 'B' and resid 150 through 154 Processing helix chain 'C' and resid 2 through 9 Processing helix chain 'C' and resid 19 through 24 Processing helix chain 'C' and resid 85 through 89 removed outlier: 3.667A pdb=" N ILE C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.542A pdb=" N GLU C 95 " --> pdb=" O PRO C 91 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET C 97 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 283 removed outlier: 3.520A pdb=" N ILE C 251 " --> pdb=" O ASP C 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE C 256 " --> pdb=" O GLN C 252 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL C 269 " --> pdb=" O GLN C 265 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS C 277 " --> pdb=" O LYS C 273 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N VAL C 278 " --> pdb=" O GLN C 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 removed outlier: 3.973A pdb=" N LEU D 28 " --> pdb=" O GLY D 24 " (cutoff:3.500A) Proline residue: D 29 - end of helix Proline residue: D 36 - end of helix Processing helix chain 'D' and resid 64 through 72 removed outlier: 3.588A pdb=" N LYS D 70 " --> pdb=" O ALA D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 85 No H-bonds generated for 'chain 'D' and resid 83 through 85' Processing helix chain 'E' and resid 2 through 28 removed outlier: 3.500A pdb=" N ILE E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 37 removed outlier: 3.579A pdb=" N ASN F 14 " --> pdb=" O ALA F 10 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU F 36 " --> pdb=" O ALA F 32 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA F 37 " --> pdb=" O THR F 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 32 removed outlier: 3.626A pdb=" N ILE G 14 " --> pdb=" O VAL G 10 " (cutoff:3.500A) Proline residue: G 15 - end of helix Processing helix chain 'H' and resid 2 through 26 removed outlier: 3.772A pdb=" N LEU H 19 " --> pdb=" O PHE H 15 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 13 removed outlier: 4.084A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 22 Processing helix chain 'I' and resid 31 through 34 Processing helix chain 'I' and resid 35 through 55 removed outlier: 3.547A pdb=" N THR I 55 " --> pdb=" O GLY I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 64 through 75 Processing helix chain 'I' and resid 78 through 107 removed outlier: 3.588A pdb=" N ALA I 90 " --> pdb=" O HIS I 86 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER I 91 " --> pdb=" O ARG I 87 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N VAL I 94 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 137 removed outlier: 3.537A pdb=" N TRP I 118 " --> pdb=" O ARG I 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER I 137 " --> pdb=" O VAL I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 removed outlier: 3.508A pdb=" N LYS I 149 " --> pdb=" O TYR I 145 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE I 150 " --> pdb=" O TRP I 146 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 158 Processing helix chain 'I' and resid 161 through 171 removed outlier: 3.524A pdb=" N LEU I 168 " --> pdb=" O PRO I 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 176 through 189 Processing helix chain 'I' and resid 189 through 210 Processing helix chain 'J' and resid 11 through 20 removed outlier: 3.680A pdb=" N LYS J 20 " --> pdb=" O ALA J 16 " (cutoff:3.500A) Processing helix chain 'J' and resid 39 through 58 Processing helix chain 'J' and resid 78 through 80 No H-bonds generated for 'chain 'J' and resid 78 through 80' Processing helix chain 'J' and resid 81 through 91 removed outlier: 3.500A pdb=" N ARG J 89 " --> pdb=" O PHE J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 93 through 109 removed outlier: 3.824A pdb=" N VAL J 104 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Proline residue: J 105 - end of helix Processing helix chain 'J' and resid 122 through 125 Processing helix chain 'J' and resid 126 through 147 Processing helix chain 'J' and resid 148 through 149 No H-bonds generated for 'chain 'J' and resid 148 through 149' Processing helix chain 'J' and resid 150 through 154 Processing helix chain 'K' and resid 2 through 9 Processing helix chain 'K' and resid 19 through 24 Processing helix chain 'K' and resid 85 through 89 removed outlier: 3.668A pdb=" N ILE K 89 " --> pdb=" O PRO K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.542A pdb=" N GLU K 95 " --> pdb=" O PRO K 91 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LYS K 96 " --> pdb=" O GLU K 92 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N MET K 97 " --> pdb=" O MET K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 283 removed outlier: 3.520A pdb=" N ILE K 251 " --> pdb=" O ASP K 247 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE K 256 " --> pdb=" O GLN K 252 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N VAL K 269 " --> pdb=" O GLN K 265 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LYS K 277 " --> pdb=" O LYS K 273 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL K 278 " --> pdb=" O GLN K 274 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 40 removed outlier: 3.973A pdb=" N LEU L 28 " --> pdb=" O GLY L 24 " (cutoff:3.500A) Proline residue: L 29 - end of helix Proline residue: L 36 - end of helix Processing helix chain 'L' and resid 64 through 72 removed outlier: 3.588A pdb=" N LYS L 70 " --> pdb=" O ALA L 66 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 85 No H-bonds generated for 'chain 'L' and resid 83 through 85' Processing helix chain 'M' and resid 2 through 28 removed outlier: 3.511A pdb=" N ILE M 28 " --> pdb=" O GLY M 24 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 37 removed outlier: 3.579A pdb=" N ASN N 14 " --> pdb=" O ALA N 10 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N GLU N 36 " --> pdb=" O ALA N 32 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA N 37 " --> pdb=" O THR N 33 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 32 removed outlier: 3.626A pdb=" N ILE O 14 " --> pdb=" O VAL O 10 " (cutoff:3.500A) Proline residue: O 15 - end of helix Processing helix chain 'P' and resid 2 through 26 removed outlier: 3.772A pdb=" N LEU P 19 " --> pdb=" O PHE P 15 " (cutoff:3.500A) Processing helix chain 'Q' and resid 33 through 43 removed outlier: 3.513A pdb=" N LYS Q 41 " --> pdb=" O TRP Q 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 43 removed outlier: 3.513A pdb=" N LYS R 41 " --> pdb=" O TRP R 37 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA2, first strand: chain 'C' and resid 32 through 34 removed outlier: 3.727A pdb=" N GLU C 82 " --> pdb=" O LEU C 131 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 38 through 39 removed outlier: 6.191A pdb=" N VAL C 71 " --> pdb=" O PRO C 117 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG C 106 " --> pdb=" O LYS C 109 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N ASN C 111 " --> pdb=" O SER C 104 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N SER C 104 " --> pdb=" O ASN C 111 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 59 through 60 Processing sheet with id=AA5, first strand: chain 'C' and resid 203 through 207 removed outlier: 3.505A pdb=" N GLU C 191 " --> pdb=" O VAL C 183 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS C 181 " --> pdb=" O ASN C 193 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 219 " --> pdb=" O VAL C 179 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 77 through 81 removed outlier: 3.683A pdb=" N THR D 78 " --> pdb=" O LEU D 90 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N VAL D 91 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE D 101 " --> pdb=" O VAL D 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 116 through 117 removed outlier: 3.628A pdb=" N ARG D 140 " --> pdb=" O GLN D 131 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 25 through 26 Processing sheet with id=AA9, first strand: chain 'K' and resid 32 through 34 removed outlier: 3.728A pdb=" N GLU K 82 " --> pdb=" O LEU K 131 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 38 through 39 removed outlier: 6.191A pdb=" N VAL K 71 " --> pdb=" O PRO K 117 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N ARG K 106 " --> pdb=" O LYS K 109 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N ASN K 111 " --> pdb=" O SER K 104 " (cutoff:3.500A) removed outlier: 9.061A pdb=" N SER K 104 " --> pdb=" O ASN K 111 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 59 through 60 Processing sheet with id=AB3, first strand: chain 'K' and resid 203 through 207 removed outlier: 3.505A pdb=" N GLU K 191 " --> pdb=" O VAL K 183 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS K 181 " --> pdb=" O ASN K 193 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU K 219 " --> pdb=" O VAL K 179 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 77 through 81 removed outlier: 3.683A pdb=" N THR L 78 " --> pdb=" O LEU L 90 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N VAL L 91 " --> pdb=" O PHE L 101 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N PHE L 101 " --> pdb=" O VAL L 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 116 through 117 removed outlier: 3.627A pdb=" N ARG L 140 " --> pdb=" O GLN L 131 " (cutoff:3.500A) 805 hydrogen bonds defined for protein. 2285 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.89 Time building geometry restraints manager: 5.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.39: 6358 1.39 - 1.59: 10180 1.59 - 1.79: 46 1.79 - 2.00: 72 2.00 - 2.20: 48 Bond restraints: 16704 Sorted by residual: bond pdb=" N GLY J 2 " pdb=" CA GLY J 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" N GLY B 2 " pdb=" CA GLY B 2 " ideal model delta sigma weight residual 1.451 1.491 -0.040 1.60e-02 3.91e+03 6.25e+00 bond pdb=" N LYS Q 32 " pdb=" CA LYS Q 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.02e+00 bond pdb=" N LYS R 32 " pdb=" CA LYS R 32 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.01e+00 bond pdb=" N MET E 1 " pdb=" CA MET E 1 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 ... (remaining 16699 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.76: 22683 2.76 - 5.51: 167 5.51 - 8.27: 2 8.27 - 11.02: 0 11.02 - 13.78: 2 Bond angle restraints: 22854 Sorted by residual: angle pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sigma weight residual 109.00 122.78 -13.78 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C3C HEC I 303 " pdb=" CAC HEC I 303 " pdb=" CBC HEC I 303 " ideal model delta sigma weight residual 109.00 122.78 -13.78 3.00e+00 1.11e-01 2.11e+01 angle pdb=" C GLN C 246 " pdb=" N ASP C 247 " pdb=" CA ASP C 247 " ideal model delta sigma weight residual 121.83 125.21 -3.38 1.56e+00 4.11e-01 4.69e+00 angle pdb=" C GLN K 246 " pdb=" N ASP K 247 " pdb=" CA ASP K 247 " ideal model delta sigma weight residual 121.83 125.14 -3.31 1.56e+00 4.11e-01 4.51e+00 angle pdb=" CA GLY L 102 " pdb=" C GLY L 102 " pdb=" N ILE L 103 " ideal model delta sigma weight residual 114.75 117.71 -2.96 1.40e+00 5.10e-01 4.47e+00 ... (remaining 22849 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.46: 9390 21.46 - 42.92: 323 42.92 - 64.38: 68 64.38 - 85.85: 24 85.85 - 107.31: 6 Dihedral angle restraints: 9811 sinusoidal: 4185 harmonic: 5626 Sorted by residual: dihedral pdb=" C2C HEC A 303 " pdb=" C3C HEC A 303 " pdb=" CAC HEC A 303 " pdb=" CBC HEC A 303 " ideal model delta sinusoidal sigma weight residual 60.00 8.21 51.79 2 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" C2C HEC I 303 " pdb=" C3C HEC I 303 " pdb=" CAC HEC I 303 " pdb=" CBC HEC I 303 " ideal model delta sinusoidal sigma weight residual 60.00 8.21 51.79 2 1.00e+01 1.00e-02 2.96e+01 dihedral pdb=" C2B HEC I 303 " pdb=" C3B HEC I 303 " pdb=" CAB HEC I 303 " pdb=" CBB HEC I 303 " ideal model delta sinusoidal sigma weight residual -120.00 -74.11 -45.89 2 1.00e+01 1.00e-02 2.47e+01 ... (remaining 9808 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1441 0.027 - 0.053: 677 0.053 - 0.080: 238 0.080 - 0.107: 116 0.107 - 0.133: 80 Chirality restraints: 2552 Sorted by residual: chirality pdb=" CA ILE G 2 " pdb=" N ILE G 2 " pdb=" C ILE G 2 " pdb=" CB ILE G 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.45e-01 chirality pdb=" CA ILE O 2 " pdb=" N ILE O 2 " pdb=" C ILE O 2 " pdb=" CB ILE O 2 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE K 51 " pdb=" N ILE K 51 " pdb=" C ILE K 51 " pdb=" CB ILE K 51 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 ... (remaining 2549 not shown) Planarity restraints: 2806 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL L 162 " -0.040 5.00e-02 4.00e+02 6.08e-02 5.92e+00 pdb=" N PRO L 163 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO L 163 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO L 163 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL D 162 " 0.040 5.00e-02 4.00e+02 6.07e-02 5.89e+00 pdb=" N PRO D 163 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 163 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 163 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR K 146 " 0.024 5.00e-02 4.00e+02 3.68e-02 2.17e+00 pdb=" N PRO K 147 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO K 147 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO K 147 " 0.020 5.00e-02 4.00e+02 ... (remaining 2803 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.58: 128 2.58 - 3.16: 13131 3.16 - 3.74: 22884 3.74 - 4.32: 34341 4.32 - 4.90: 57244 Nonbonded interactions: 127728 Sorted by model distance: nonbonded pdb=" OD2 ASP B 35 " pdb=" O HOH B 301 " model vdw 1.994 3.040 nonbonded pdb=" OD2 ASP J 35 " pdb=" O HOH J 301 " model vdw 1.996 3.040 nonbonded pdb=" OD1 ASP J 35 " pdb=" O HOH J 302 " model vdw 2.022 3.040 nonbonded pdb=" OD1 ASP B 35 " pdb=" O HOH B 302 " model vdw 2.023 3.040 nonbonded pdb=" SG CYS L 112 " pdb=" SG CYS L 127 " model vdw 2.033 3.760 ... (remaining 127723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'J' } ncs_group { reference = chain 'C' selection = chain 'K' } ncs_group { reference = chain 'D' selection = chain 'L' } ncs_group { reference = chain 'E' selection = chain 'M' } ncs_group { reference = (chain 'F' and (resid 1 through 6 or resid 8 through 37)) selection = (chain 'N' and (resid 1 through 6 or resid 8 through 37)) } ncs_group { reference = chain 'G' selection = chain 'O' } ncs_group { reference = chain 'H' selection = chain 'P' } ncs_group { reference = chain 'Q' selection = chain 'R' } 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=0.40 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: 3.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.700 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 43.120 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 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 : 0.003 0.052 16704 Z= 0.223 Angle : 0.534 13.775 22854 Z= 0.243 Chirality : 0.042 0.133 2552 Planarity : 0.004 0.061 2806 Dihedral : 12.293 107.306 6204 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.61 % Allowed : 2.66 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.19), residues: 1940 helix: 1.22 (0.16), residues: 924 sheet: -0.51 (0.32), residues: 258 loop : -0.62 (0.23), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 164 HIS 0.004 0.001 HIS A 202 PHE 0.011 0.001 PHE C 128 TYR 0.010 0.001 TYR I 136 ARG 0.003 0.000 ARG K 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 202 time to evaluate : 1.912 Fit side-chains REVERT: A 75 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.7834 (mp0) REVERT: A 156 ASP cc_start: 0.8624 (t0) cc_final: 0.8270 (t0) REVERT: C 181 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8897 (ttpp) REVERT: D 8 ASN cc_start: 0.8745 (t0) cc_final: 0.8243 (t0) REVERT: I 75 GLU cc_start: 0.8985 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: I 156 ASP cc_start: 0.8624 (t0) cc_final: 0.8269 (t0) REVERT: K 56 GLN cc_start: 0.8180 (mm-40) cc_final: 0.7848 (mm110) REVERT: L 8 ASN cc_start: 0.8746 (t0) cc_final: 0.8241 (t0) outliers start: 10 outliers final: 8 residues processed: 210 average time/residue: 1.7460 time to fit residues: 397.4879 Evaluate side-chains 177 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 167 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 54 ASP Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 54 ASP Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 3.9990 chunk 140 optimal weight: 8.9990 chunk 78 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 0.7980 chunk 75 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 88 optimal weight: 0.7980 chunk 108 optimal weight: 0.7980 chunk 168 optimal weight: 2.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN C 99 ASN D 121 ASN J 118 ASN K 99 ASN L 121 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16704 Z= 0.316 Angle : 0.729 10.890 22854 Z= 0.352 Chirality : 0.048 0.172 2552 Planarity : 0.006 0.067 2806 Dihedral : 12.454 97.365 2702 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.03 % Allowed : 7.26 % Favored : 91.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.23 (0.20), residues: 1940 helix: 2.19 (0.17), residues: 968 sheet: -0.12 (0.32), residues: 238 loop : -0.74 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 146 HIS 0.007 0.002 HIS I 202 PHE 0.016 0.002 PHE C 128 TYR 0.016 0.002 TYR I 136 ARG 0.008 0.001 ARG D 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 1.742 Fit side-chains REVERT: A 156 ASP cc_start: 0.8754 (t0) cc_final: 0.8358 (t0) REVERT: C 181 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8788 (ttpp) REVERT: D 8 ASN cc_start: 0.8788 (t0) cc_final: 0.8245 (t0) REVERT: I 156 ASP cc_start: 0.8752 (t0) cc_final: 0.8357 (t0) REVERT: L 8 ASN cc_start: 0.8788 (t0) cc_final: 0.8245 (t0) outliers start: 17 outliers final: 6 residues processed: 177 average time/residue: 1.8899 time to fit residues: 361.6260 Evaluate side-chains 160 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 154 time to evaluate : 1.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 93 optimal weight: 0.0570 chunk 52 optimal weight: 0.0370 chunk 140 optimal weight: 0.0030 chunk 115 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 169 optimal weight: 10.0000 chunk 182 optimal weight: 9.9990 chunk 150 optimal weight: 1.9990 chunk 167 optimal weight: 6.9990 chunk 57 optimal weight: 0.5980 chunk 135 optimal weight: 3.9990 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN D 121 ASN J 118 ASN K 56 GLN L 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16704 Z= 0.174 Angle : 0.581 8.771 22854 Z= 0.275 Chirality : 0.043 0.169 2552 Planarity : 0.005 0.067 2806 Dihedral : 10.823 83.476 2692 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.57 % Allowed : 7.87 % Favored : 90.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.54 (0.20), residues: 1940 helix: 2.60 (0.17), residues: 966 sheet: 0.09 (0.32), residues: 238 loop : -0.85 (0.22), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 146 HIS 0.003 0.001 HIS A 202 PHE 0.010 0.001 PHE L 123 TYR 0.008 0.001 TYR C 53 ARG 0.006 0.000 ARG K 50 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 1.817 Fit side-chains REVERT: A 75 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.7962 (mp0) REVERT: A 131 PHE cc_start: 0.8608 (OUTLIER) cc_final: 0.6846 (t80) REVERT: A 156 ASP cc_start: 0.8738 (t0) cc_final: 0.8310 (t0) REVERT: C 181 LYS cc_start: 0.9084 (ttpp) cc_final: 0.8806 (ttpp) REVERT: D 8 ASN cc_start: 0.8841 (t0) cc_final: 0.8293 (t0) REVERT: I 75 GLU cc_start: 0.8829 (OUTLIER) cc_final: 0.7954 (mp0) REVERT: I 131 PHE cc_start: 0.8610 (OUTLIER) cc_final: 0.6847 (t80) REVERT: I 156 ASP cc_start: 0.8737 (t0) cc_final: 0.8310 (t0) REVERT: L 8 ASN cc_start: 0.8842 (t0) cc_final: 0.8294 (t0) REVERT: Q 50 GLU cc_start: 0.7811 (tt0) cc_final: 0.7394 (tt0) outliers start: 26 outliers final: 8 residues processed: 194 average time/residue: 1.7386 time to fit residues: 366.4102 Evaluate side-chains 163 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 1.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 167 optimal weight: 8.9990 chunk 127 optimal weight: 0.7980 chunk 87 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 20.0000 chunk 179 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN L 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16704 Z= 0.234 Angle : 0.623 9.863 22854 Z= 0.293 Chirality : 0.045 0.158 2552 Planarity : 0.005 0.068 2806 Dihedral : 10.974 84.248 2692 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.63 % Allowed : 9.44 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.54 (0.19), residues: 1940 helix: 2.61 (0.17), residues: 968 sheet: 0.06 (0.32), residues: 238 loop : -0.86 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 164 HIS 0.007 0.001 HIS I 202 PHE 0.013 0.002 PHE K 128 TYR 0.009 0.001 TYR A 105 ARG 0.006 0.000 ARG C 50 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 155 time to evaluate : 1.920 Fit side-chains REVERT: A 75 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7897 (mp0) REVERT: A 156 ASP cc_start: 0.8746 (t0) cc_final: 0.8295 (t0) REVERT: C 181 LYS cc_start: 0.9092 (ttpp) cc_final: 0.8798 (ttpp) REVERT: D 8 ASN cc_start: 0.8853 (t0) cc_final: 0.8288 (t0) REVERT: I 75 GLU cc_start: 0.8859 (OUTLIER) cc_final: 0.7931 (mp0) REVERT: I 156 ASP cc_start: 0.8746 (t0) cc_final: 0.8295 (t0) REVERT: L 8 ASN cc_start: 0.8853 (t0) cc_final: 0.8284 (t0) outliers start: 27 outliers final: 12 residues processed: 174 average time/residue: 1.8793 time to fit residues: 353.4272 Evaluate side-chains 166 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 152 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 149 optimal weight: 10.0000 chunk 102 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 133 optimal weight: 5.9990 chunk 74 optimal weight: 5.9990 chunk 153 optimal weight: 3.9990 chunk 124 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 1.9990 chunk 161 optimal weight: 10.0000 chunk 45 optimal weight: 5.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 56 GLN K 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16704 Z= 0.273 Angle : 0.647 9.707 22854 Z= 0.307 Chirality : 0.046 0.151 2552 Planarity : 0.005 0.070 2806 Dihedral : 11.044 84.424 2692 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.18 % Allowed : 9.62 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.19), residues: 1940 helix: 2.52 (0.17), residues: 968 sheet: -0.02 (0.32), residues: 238 loop : -0.92 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 164 HIS 0.008 0.001 HIS A 202 PHE 0.015 0.002 PHE C 128 TYR 0.009 0.001 TYR C 146 ARG 0.005 0.000 ARG K 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 2.159 Fit side-chains REVERT: A 75 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7849 (mp0) REVERT: A 156 ASP cc_start: 0.8746 (t0) cc_final: 0.8299 (t0) REVERT: C 181 LYS cc_start: 0.9073 (ttpp) cc_final: 0.8772 (ttpp) REVERT: D 8 ASN cc_start: 0.8877 (t0) cc_final: 0.8283 (t0) REVERT: I 75 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.7846 (mp0) REVERT: I 156 ASP cc_start: 0.8747 (t0) cc_final: 0.8300 (t0) REVERT: K 55 MET cc_start: 0.8481 (OUTLIER) cc_final: 0.7888 (mmt) REVERT: L 8 ASN cc_start: 0.8877 (t0) cc_final: 0.8281 (t0) outliers start: 36 outliers final: 17 residues processed: 193 average time/residue: 1.7388 time to fit residues: 364.8426 Evaluate side-chains 171 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 55 MET Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 60 optimal weight: 3.9990 chunk 161 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 105 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 83 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 118 ASN D 121 ASN J 118 ASN K 56 GLN L 121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 16704 Z= 0.296 Angle : 0.667 9.626 22854 Z= 0.317 Chirality : 0.046 0.151 2552 Planarity : 0.005 0.070 2806 Dihedral : 11.113 84.654 2692 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.00 % Allowed : 10.41 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.30 (0.19), residues: 1940 helix: 2.45 (0.17), residues: 968 sheet: -0.15 (0.33), residues: 230 loop : -0.99 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP L 164 HIS 0.008 0.001 HIS I 202 PHE 0.015 0.002 PHE K 128 TYR 0.010 0.001 TYR I 105 ARG 0.006 0.001 ARG K 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.951 Fit side-chains REVERT: A 75 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.7833 (mp0) REVERT: A 156 ASP cc_start: 0.8753 (t0) cc_final: 0.8333 (t0) REVERT: C 181 LYS cc_start: 0.9082 (ttpp) cc_final: 0.8782 (ttpp) REVERT: D 8 ASN cc_start: 0.8880 (t0) cc_final: 0.8274 (t0) REVERT: D 155 ASP cc_start: 0.6377 (OUTLIER) cc_final: 0.5838 (t70) REVERT: I 156 ASP cc_start: 0.8751 (t0) cc_final: 0.8333 (t0) REVERT: K 55 MET cc_start: 0.8466 (OUTLIER) cc_final: 0.7860 (mmt) REVERT: L 8 ASN cc_start: 0.8859 (t0) cc_final: 0.8255 (t0) outliers start: 33 outliers final: 19 residues processed: 177 average time/residue: 1.8362 time to fit residues: 351.2433 Evaluate side-chains 170 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 97 MET Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 55 MET Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 173 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 101 optimal weight: 0.6980 chunk 151 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 179 optimal weight: 2.9990 chunk 112 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN L 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16704 Z= 0.190 Angle : 0.598 10.578 22854 Z= 0.284 Chirality : 0.044 0.150 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.671 82.760 2692 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 1.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.18 % Allowed : 10.53 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.58 (0.20), residues: 1940 helix: 2.70 (0.17), residues: 966 sheet: -0.09 (0.32), residues: 240 loop : -0.86 (0.22), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 118 HIS 0.006 0.001 HIS L 151 PHE 0.010 0.001 PHE I 52 TYR 0.009 0.001 TYR A 105 ARG 0.007 0.000 ARG K 184 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 1.694 Fit side-chains REVERT: A 75 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: A 131 PHE cc_start: 0.8671 (OUTLIER) cc_final: 0.6817 (t80) REVERT: A 156 ASP cc_start: 0.8731 (t0) cc_final: 0.8322 (t0) REVERT: C 181 LYS cc_start: 0.9054 (ttpp) cc_final: 0.8767 (ttpp) REVERT: D 8 ASN cc_start: 0.8868 (t0) cc_final: 0.8283 (t0) REVERT: D 155 ASP cc_start: 0.6389 (OUTLIER) cc_final: 0.5848 (t70) REVERT: I 75 GLU cc_start: 0.8797 (OUTLIER) cc_final: 0.7797 (mp0) REVERT: I 131 PHE cc_start: 0.8672 (OUTLIER) cc_final: 0.6818 (t80) REVERT: I 156 ASP cc_start: 0.8730 (t0) cc_final: 0.8322 (t0) REVERT: L 8 ASN cc_start: 0.8863 (t0) cc_final: 0.8283 (t0) REVERT: L 155 ASP cc_start: 0.6400 (OUTLIER) cc_final: 0.5866 (t70) outliers start: 36 outliers final: 19 residues processed: 191 average time/residue: 1.6493 time to fit residues: 342.9681 Evaluate side-chains 181 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain A residue 163 SER Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain B residue 155 LEU Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain I residue 163 SER Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain J residue 155 LEU Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 97 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 113 optimal weight: 0.8980 chunk 122 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 140 optimal weight: 0.0770 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16704 Z= 0.186 Angle : 0.595 9.200 22854 Z= 0.279 Chirality : 0.043 0.152 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.449 82.336 2692 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.12 % Allowed : 10.84 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.72 (0.20), residues: 1940 helix: 2.77 (0.17), residues: 976 sheet: 0.10 (0.34), residues: 220 loop : -0.80 (0.22), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 146 HIS 0.007 0.001 HIS L 151 PHE 0.010 0.001 PHE I 52 TYR 0.008 0.001 TYR I 105 ARG 0.007 0.000 ARG K 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 158 time to evaluate : 1.857 Fit side-chains REVERT: A 75 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: A 131 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.6717 (t80) REVERT: A 156 ASP cc_start: 0.8731 (t0) cc_final: 0.8391 (t0) REVERT: C 181 LYS cc_start: 0.9055 (ttpp) cc_final: 0.8780 (ttpp) REVERT: D 8 ASN cc_start: 0.8853 (t0) cc_final: 0.8251 (t0) REVERT: D 155 ASP cc_start: 0.6388 (OUTLIER) cc_final: 0.5830 (t70) REVERT: I 75 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7840 (mp0) REVERT: I 131 PHE cc_start: 0.8646 (OUTLIER) cc_final: 0.6718 (t80) REVERT: I 156 ASP cc_start: 0.8730 (t0) cc_final: 0.8392 (t0) REVERT: L 8 ASN cc_start: 0.8851 (t0) cc_final: 0.8273 (t0) REVERT: L 155 ASP cc_start: 0.6413 (OUTLIER) cc_final: 0.5862 (t70) outliers start: 35 outliers final: 13 residues processed: 188 average time/residue: 1.6596 time to fit residues: 340.5459 Evaluate side-chains 175 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 64 GLU Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 97 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain E residue 26 ASN Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 64 GLU Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 163 optimal weight: 2.9990 chunk 171 optimal weight: 0.0060 chunk 156 optimal weight: 1.9990 chunk 167 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 131 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 158 optimal weight: 0.0010 chunk 166 optimal weight: 0.8980 overall best weight: 0.5002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 ASN L 121 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16704 Z= 0.173 Angle : 0.582 8.837 22854 Z= 0.276 Chirality : 0.043 0.147 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.197 81.769 2692 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.27 % Allowed : 12.17 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.85 (0.20), residues: 1940 helix: 2.87 (0.17), residues: 978 sheet: 0.17 (0.34), residues: 220 loop : -0.77 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 146 HIS 0.008 0.001 HIS L 151 PHE 0.010 0.001 PHE A 131 TYR 0.007 0.001 TYR C 53 ARG 0.009 0.000 ARG K 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 162 time to evaluate : 1.664 Fit side-chains REVERT: A 75 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7788 (mp0) REVERT: A 131 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.6734 (t80) REVERT: A 156 ASP cc_start: 0.8728 (t0) cc_final: 0.8397 (t0) REVERT: C 181 LYS cc_start: 0.9049 (ttpp) cc_final: 0.8782 (ttpp) REVERT: D 8 ASN cc_start: 0.8816 (t0) cc_final: 0.8254 (t0) REVERT: I 75 GLU cc_start: 0.8729 (OUTLIER) cc_final: 0.7791 (mp0) REVERT: I 131 PHE cc_start: 0.8575 (OUTLIER) cc_final: 0.6732 (t80) REVERT: I 156 ASP cc_start: 0.8728 (t0) cc_final: 0.8398 (t0) REVERT: L 8 ASN cc_start: 0.8815 (t0) cc_final: 0.8251 (t0) REVERT: L 155 ASP cc_start: 0.6264 (OUTLIER) cc_final: 0.5807 (t0) outliers start: 21 outliers final: 9 residues processed: 177 average time/residue: 1.7781 time to fit residues: 340.8593 Evaluate side-chains 174 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain B residue 119 LYS Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain J residue 119 LYS Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 109 optimal weight: 4.9990 chunk 176 optimal weight: 0.9990 chunk 107 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 185 optimal weight: 0.1980 chunk 170 optimal weight: 10.0000 chunk 147 optimal weight: 2.9990 chunk 15 optimal weight: 0.0370 chunk 113 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16704 Z= 0.184 Angle : 0.592 9.157 22854 Z= 0.279 Chirality : 0.043 0.150 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.157 82.103 2692 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.15 % Allowed : 12.11 % Favored : 86.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.85 (0.20), residues: 1940 helix: 2.87 (0.17), residues: 978 sheet: 0.20 (0.34), residues: 220 loop : -0.77 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 118 HIS 0.004 0.001 HIS A 202 PHE 0.010 0.001 PHE I 198 TYR 0.008 0.001 TYR I 105 ARG 0.009 0.000 ARG K 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3880 Ramachandran restraints generated. 1940 Oldfield, 0 Emsley, 1940 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 161 time to evaluate : 1.944 Fit side-chains REVERT: A 75 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.7820 (mp0) REVERT: A 131 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.6741 (t80) REVERT: A 156 ASP cc_start: 0.8703 (t0) cc_final: 0.8378 (t0) REVERT: D 8 ASN cc_start: 0.8811 (t0) cc_final: 0.8256 (t0) REVERT: D 155 ASP cc_start: 0.6255 (OUTLIER) cc_final: 0.5800 (t70) REVERT: I 6 ASP cc_start: 0.8726 (m-30) cc_final: 0.8310 (m-30) REVERT: I 75 GLU cc_start: 0.8739 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: I 131 PHE cc_start: 0.8628 (OUTLIER) cc_final: 0.6740 (t80) REVERT: I 156 ASP cc_start: 0.8703 (t0) cc_final: 0.8379 (t0) REVERT: L 8 ASN cc_start: 0.8809 (t0) cc_final: 0.8249 (t0) REVERT: L 155 ASP cc_start: 0.6268 (OUTLIER) cc_final: 0.5815 (t0) outliers start: 19 outliers final: 7 residues processed: 176 average time/residue: 1.7174 time to fit residues: 328.5054 Evaluate side-chains 172 residues out of total 1648 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 159 time to evaluate : 1.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 GLU Chi-restraints excluded: chain A residue 131 PHE Chi-restraints excluded: chain C residue 183 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 155 ASP Chi-restraints excluded: chain I residue 75 GLU Chi-restraints excluded: chain I residue 131 PHE Chi-restraints excluded: chain K residue 183 VAL Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 155 ASP Chi-restraints excluded: chain M residue 26 ASN Chi-restraints excluded: chain Q residue 38 LEU Chi-restraints excluded: chain R residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 117 optimal weight: 0.7980 chunk 157 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 136 optimal weight: 5.9990 chunk 21 optimal weight: 0.2980 chunk 41 optimal weight: 0.9980 chunk 147 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 151 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN D 121 ASN L 121 ASN ** L 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.110854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072811 restraints weight = 45578.840| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.78 r_work: 0.2892 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2784 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16704 Z= 0.194 Angle : 0.602 9.380 22854 Z= 0.285 Chirality : 0.043 0.151 2552 Planarity : 0.005 0.069 2806 Dihedral : 10.113 82.304 2684 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.73 % Allowed : 12.77 % Favored : 86.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 1.82 (0.20), residues: 1940 helix: 2.85 (0.17), residues: 978 sheet: 0.20 (0.34), residues: 220 loop : -0.78 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 146 HIS 0.008 0.001 HIS D 151 PHE 0.011 0.001 PHE A 52 TYR 0.009 0.001 TYR I 105 ARG 0.009 0.001 ARG K 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6891.54 seconds wall clock time: 124 minutes 11.77 seconds (7451.77 seconds total)