Starting phenix.real_space_refine on Thu Sep 18 05:52:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ys5_39556/09_2025/8ys5_39556.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ys5_39556/09_2025/8ys5_39556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ys5_39556/09_2025/8ys5_39556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ys5_39556/09_2025/8ys5_39556.map" model { file = "/net/cci-nas-00/data/ceres_data/8ys5_39556/09_2025/8ys5_39556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ys5_39556/09_2025/8ys5_39556.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.121 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 24 7.16 5 P 4 5.49 5 Mg 2 5.21 5 S 128 5.16 5 C 9240 2.51 5 N 2468 2.21 5 O 2752 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14618 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "A" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2907 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 353} Chain: "C" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2132 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 264} Chain: "B" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1405 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 6, 'TRANS': 177} Chain: "F" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "G" Number of atoms: 2907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2907 Classifications: {'peptide': 374} Link IDs: {'PCIS': 3, 'PTRANS': 17, 'TRANS': 353} Chain: "H" Number of atoms: 2132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2132 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 264} Chain: "I" Number of atoms: 1405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1405 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 6, 'TRANS': 177} Chain: "D" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'SF4': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Unusual residues: {'SF4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 35 Unusual residues: {' MG': 1, 'SF4': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 108 SG CYS D 19 34.509 71.759 110.129 1.00 34.35 S ATOM 149 SG CYS D 25 33.240 77.549 108.560 0.75 23.97 S ATOM 442 SG CYS D 66 30.951 72.979 104.417 0.47 17.95 S ATOM 127 SG CYS D 22 36.769 74.381 104.568 0.48 30.53 S ATOM 387 SG CYS D 59 25.423 86.573 105.969 0.46 37.87 S ATOM 369 SG CYS D 56 22.882 83.291 110.545 0.50 35.92 S ATOM 175 SG CYS D 29 29.427 84.958 109.995 0.68 40.33 S ATOM 409 SG CYS D 62 26.832 80.290 106.339 0.69 30.17 S ATOM 3887 SG CYS C 19 44.255 67.173 99.087 1.00 37.58 S ATOM 3911 SG CYS C 22 40.121 70.356 95.358 1.00 38.88 S ATOM 4135 SG CYS C 53 43.066 65.615 92.800 1.00 27.58 S ATOM 5266 SG CYS C 202 46.324 71.045 94.284 1.00 17.49 S ATOM 7366 SG CYS F 19 54.993 71.703 29.225 1.00 89.55 S ATOM 7407 SG CYS F 25 53.690 77.587 30.216 0.55 91.54 S ATOM 7700 SG CYS F 66 57.475 74.759 34.687 0.53 78.57 S ATOM 7385 SG CYS F 22 51.459 73.445 34.527 0.57 88.93 S ATOM 7645 SG CYS F 59 57.171 89.099 32.059 0.26106.57 S ATOM 7627 SG CYS F 56 61.050 86.441 27.611 0.52108.45 S ATOM 7433 SG CYS F 29 54.177 85.994 28.147 0.39 99.13 S ATOM 7667 SG CYS F 62 56.329 83.366 31.672 0.24 93.10 S ATOM 11145 SG CYS H 19 47.567 64.623 40.965 1.00 96.05 S ATOM 11169 SG CYS H 22 49.604 69.733 44.218 1.00 88.51 S ATOM 11393 SG CYS H 53 49.349 64.624 47.338 1.00 93.49 S ATOM 12524 SG CYS H 202 43.857 67.731 45.412 1.00 74.05 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N GLY F 35 " occ=0.07 ... (2 atoms not shown) pdb=" O GLY F 35 " occ=0.00 residue: pdb=" N GLY I 90 " occ=0.59 ... (2 atoms not shown) pdb=" O GLY I 90 " occ=0.85 Time building chain proxies: 3.89, per 1000 atoms: 0.27 Number of scatterers: 14618 At special positions: 0 Unit cell: (96.76, 109.06, 142.68, 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) Fe 24 26.01 S 128 16.00 P 4 15.00 Mg 2 11.99 O 2752 8.00 N 2468 7.00 C 9240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.41 Conformation dependent library (CDL) restraints added in 746.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 C 301 " pdb="FE4 SF4 C 301 " - pdb=" SG CYS C 202 " pdb="FE3 SF4 C 301 " - pdb=" SG CYS C 53 " pdb="FE1 SF4 C 301 " - pdb=" SG CYS C 19 " pdb="FE2 SF4 C 301 " - pdb=" SG CYS C 22 " pdb=" SF4 D 201 " pdb="FE4 SF4 D 201 " - pdb=" SG CYS D 22 " pdb="FE2 SF4 D 201 " - pdb=" SG CYS D 25 " pdb="FE1 SF4 D 201 " - pdb=" SG CYS D 19 " pdb="FE3 SF4 D 201 " - pdb=" SG CYS D 66 " pdb=" SF4 D 202 " pdb="FE3 SF4 D 202 " - pdb=" SG CYS D 29 " pdb="FE2 SF4 D 202 " - pdb=" SG CYS D 56 " pdb="FE4 SF4 D 202 " - pdb=" SG CYS D 62 " pdb="FE1 SF4 D 202 " - pdb=" SG CYS D 59 " pdb=" SF4 F 201 " pdb="FE2 SF4 F 201 " - pdb=" SG CYS F 25 " pdb="FE4 SF4 F 201 " - pdb=" SG CYS F 22 " pdb="FE1 SF4 F 201 " - pdb=" SG CYS F 19 " pdb="FE3 SF4 F 201 " - pdb=" SG CYS F 66 " pdb=" SF4 F 202 " pdb="FE4 SF4 F 202 " - pdb=" SG CYS F 62 " pdb="FE3 SF4 F 202 " - pdb=" SG CYS F 29 " pdb="FE2 SF4 F 202 " - pdb=" SG CYS F 56 " pdb="FE1 SF4 F 202 " - pdb=" SG CYS F 59 " pdb=" SF4 H 301 " pdb="FE2 SF4 H 301 " - pdb=" SG CYS H 22 " pdb="FE4 SF4 H 301 " - pdb=" SG CYS H 202 " pdb="FE3 SF4 H 301 " - pdb=" SG CYS H 53 " pdb="FE1 SF4 H 301 " - pdb=" SG CYS H 19 " Number of angles added : 72 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3428 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 17 sheets defined 43.8% alpha, 13.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing helix chain 'D' and resid 23 through 28 removed outlier: 3.610A pdb=" N VAL D 28 " --> pdb=" O ILE D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 56 Processing helix chain 'D' and resid 60 through 66 Processing helix chain 'D' and resid 85 through 97 removed outlier: 3.564A pdb=" N GLN D 89 " --> pdb=" O SER D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 109 removed outlier: 3.868A pdb=" N GLU D 109 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 8 through 20 Processing helix chain 'A' and resid 33 through 43 removed outlier: 3.641A pdb=" N VAL A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 47 removed outlier: 3.519A pdb=" N GLY A 47 " --> pdb=" O PRO A 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 44 through 47' Processing helix chain 'A' and resid 55 through 69 removed outlier: 3.732A pdb=" N SER A 63 " --> pdb=" O GLY A 59 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N SER A 69 " --> pdb=" O GLY A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 95 removed outlier: 3.521A pdb=" N VAL A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N GLU A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLN A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLY A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N TYR A 91 " --> pdb=" O GLU A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.844A pdb=" N HIS A 127 " --> pdb=" O ASN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 161 removed outlier: 4.142A pdb=" N THR A 148 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR A 150 " --> pdb=" O ALA A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 183 through 191 Processing helix chain 'A' and resid 242 through 259 removed outlier: 3.861A pdb=" N ILE A 250 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ASP A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ILE A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 265 removed outlier: 4.005A pdb=" N ASN A 265 " --> pdb=" O GLN A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 296 removed outlier: 3.942A pdb=" N ALA A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLU A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP A 295 " --> pdb=" O GLU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 327 removed outlier: 3.636A pdb=" N GLU A 322 " --> pdb=" O LYS A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 365 through 374 removed outlier: 3.917A pdb=" N GLU A 374 " --> pdb=" O ALA A 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 38 Processing helix chain 'C' and resid 41 through 43 No H-bonds generated for 'chain 'C' and resid 41 through 43' Processing helix chain 'C' and resid 54 through 60 removed outlier: 3.512A pdb=" N MET C 57 " --> pdb=" O SER C 54 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N TYR C 60 " --> pdb=" O MET C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 84 Processing helix chain 'C' and resid 102 through 113 Processing helix chain 'C' and resid 156 through 165 Processing helix chain 'C' and resid 176 through 189 removed outlier: 3.662A pdb=" N SER C 189 " --> pdb=" O LYS C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 211 removed outlier: 3.851A pdb=" N LYS C 209 " --> pdb=" O LEU C 206 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N LYS C 211 " --> pdb=" O ARG C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 214 through 225 Processing helix chain 'C' and resid 228 through 234 Processing helix chain 'C' and resid 236 through 240 removed outlier: 3.592A pdb=" N ARG C 240 " --> pdb=" O PRO C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 removed outlier: 3.693A pdb=" N GLU C 264 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN C 270 " --> pdb=" O ILE C 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 16 No H-bonds generated for 'chain 'B' and resid 14 through 16' Processing helix chain 'B' and resid 17 through 30 removed outlier: 4.232A pdb=" N ILE B 21 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N LEU B 22 " --> pdb=" O ALA B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 83 removed outlier: 3.818A pdb=" N GLN B 82 " --> pdb=" O ILE B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 110 Processing helix chain 'B' and resid 116 through 124 Processing helix chain 'B' and resid 130 through 144 removed outlier: 3.590A pdb=" N GLU B 141 " --> pdb=" O ALA B 137 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 157 Processing helix chain 'B' and resid 158 through 159 No H-bonds generated for 'chain 'B' and resid 158 through 159' Processing helix chain 'B' and resid 160 through 162 No H-bonds generated for 'chain 'B' and resid 160 through 162' Processing helix chain 'B' and resid 163 through 181 Processing helix chain 'F' and resid 24 through 28 removed outlier: 3.592A pdb=" N VAL F 28 " --> pdb=" O CYS F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 56 Processing helix chain 'F' and resid 60 through 65 Processing helix chain 'F' and resid 85 through 97 Processing helix chain 'F' and resid 103 through 109 removed outlier: 3.903A pdb=" N GLU F 109 " --> pdb=" O THR F 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 8 through 20 Processing helix chain 'G' and resid 32 through 46 removed outlier: 3.913A pdb=" N MET G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) Proline residue: G 44 - end of helix Processing helix chain 'G' and resid 55 through 69 removed outlier: 3.789A pdb=" N SER G 63 " --> pdb=" O GLY G 59 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER G 69 " --> pdb=" O GLY G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 84 Processing helix chain 'G' and resid 85 through 95 removed outlier: 3.785A pdb=" N GLY G 90 " --> pdb=" O VAL G 86 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TYR G 91 " --> pdb=" O GLU G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 127 removed outlier: 3.931A pdb=" N HIS G 127 " --> pdb=" O ASN G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 144 through 161 removed outlier: 4.103A pdb=" N THR G 148 " --> pdb=" O GLU G 144 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N THR G 150 " --> pdb=" O ALA G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 169 through 175 Processing helix chain 'G' and resid 183 through 190 Processing helix chain 'G' and resid 242 through 259 removed outlier: 3.613A pdb=" N ILE G 250 " --> pdb=" O GLY G 246 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE G 257 " --> pdb=" O LEU G 253 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 265 removed outlier: 3.505A pdb=" N ASN G 265 " --> pdb=" O GLN G 261 " (cutoff:3.500A) Processing helix chain 'G' and resid 284 through 297 removed outlier: 3.902A pdb=" N ALA G 288 " --> pdb=" O SER G 284 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU G 291 " --> pdb=" O LEU G 287 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 327 removed outlier: 3.586A pdb=" N GLU G 322 " --> pdb=" O LYS G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 340 through 347 Processing helix chain 'G' and resid 348 through 350 No H-bonds generated for 'chain 'G' and resid 348 through 350' Processing helix chain 'G' and resid 365 through 374 removed outlier: 3.519A pdb=" N LYS G 373 " --> pdb=" O ILE G 369 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLU G 374 " --> pdb=" O ALA G 370 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 38 Processing helix chain 'H' and resid 41 through 43 No H-bonds generated for 'chain 'H' and resid 41 through 43' Processing helix chain 'H' and resid 54 through 60 removed outlier: 3.511A pdb=" N MET H 57 " --> pdb=" O SER H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 84 Processing helix chain 'H' and resid 102 through 113 Processing helix chain 'H' and resid 156 through 165 Processing helix chain 'H' and resid 176 through 189 removed outlier: 3.842A pdb=" N SER H 189 " --> pdb=" O LYS H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 214 through 226 Processing helix chain 'H' and resid 228 through 234 Processing helix chain 'H' and resid 257 through 270 removed outlier: 3.677A pdb=" N GLU H 264 " --> pdb=" O GLU H 260 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLN H 270 " --> pdb=" O ILE H 266 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 17 Processing helix chain 'I' and resid 18 through 30 removed outlier: 4.094A pdb=" N LEU I 22 " --> pdb=" O ALA I 18 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ALA I 23 " --> pdb=" O GLY I 19 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 81 Processing helix chain 'I' and resid 103 through 110 Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'I' and resid 130 through 144 removed outlier: 4.694A pdb=" N GLU I 141 " --> pdb=" O ALA I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 157 removed outlier: 3.667A pdb=" N VAL I 151 " --> pdb=" O GLU I 147 " (cutoff:3.500A) Processing helix chain 'I' and resid 160 through 182 removed outlier: 3.518A pdb=" N ALA I 164 " --> pdb=" O PRO I 160 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP I 165 " --> pdb=" O ALA I 161 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N THR I 166 " --> pdb=" O LYS I 162 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 12 through 14 Processing sheet with id=AA2, first strand: chain 'D' and resid 34 through 38 Processing sheet with id=AA3, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'A' and resid 23 through 26 removed outlier: 3.778A pdb=" N GLY A 26 " --> pdb=" O ILE A 51 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.859A pdb=" N THR A 75 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 227 through 228 removed outlier: 6.550A pdb=" N VAL A 228 " --> pdb=" O HIS H 67 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN H 64 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N CYS H 46 " --> pdb=" O ILE H 90 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N VAL H 92 " --> pdb=" O CYS H 46 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL H 48 " --> pdb=" O VAL H 92 " (cutoff:3.500A) removed outlier: 8.940A pdb=" N GLY H 94 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN H 117 " --> pdb=" O VAL H 89 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL H 91 " --> pdb=" O ASN H 117 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N VAL H 169 " --> pdb=" O LEU H 249 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 267 through 270 removed outlier: 6.428A pdb=" N ILE A 277 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N PHE A 307 " --> pdb=" O ILE A 277 " (cutoff:3.500A) removed outlier: 5.898A pdb=" N VAL A 278 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE A 333 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ILE A 330 " --> pdb=" O HIS A 353 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N PHE A 355 " --> pdb=" O ILE A 330 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N VAL A 332 " --> pdb=" O PHE A 355 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 247 through 251 removed outlier: 5.040A pdb=" N VAL C 248 " --> pdb=" O ARG C 171 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ARG C 171 " --> pdb=" O VAL C 248 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N PHE C 168 " --> pdb=" O PHE C 195 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ASP C 197 " --> pdb=" O PHE C 168 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N ALA C 170 " --> pdb=" O ASP C 197 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N HIS C 199 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N GLU C 172 " --> pdb=" O HIS C 199 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N CYS C 46 " --> pdb=" O ILE C 90 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N VAL C 92 " --> pdb=" O CYS C 46 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N VAL C 48 " --> pdb=" O VAL C 92 " (cutoff:3.500A) removed outlier: 9.063A pdb=" N GLY C 94 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN C 64 " --> pdb=" O VAL C 45 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 125 through 126 removed outlier: 3.771A pdb=" N TYR C 126 " --> pdb=" O GLN C 132 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN C 132 " --> pdb=" O TYR C 126 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 226 through 227 Processing sheet with id=AB2, first strand: chain 'B' and resid 32 through 38 removed outlier: 7.083A pdb=" N GLN B 4 " --> pdb=" O ILE B 69 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ASP B 70 " --> pdb=" O GLY B 90 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=AB4, first strand: chain 'F' and resid 34 through 38 Processing sheet with id=AB5, first strand: chain 'G' and resid 2 through 7 Processing sheet with id=AB6, first strand: chain 'G' and resid 49 through 51 removed outlier: 6.235A pdb=" N PHE G 24 " --> pdb=" O ILE G 51 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N PHE G 23 " --> pdb=" O MET G 74 " (cutoff:3.500A) removed outlier: 8.348A pdb=" N ALA G 76 " --> pdb=" O PHE G 23 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N GLY G 25 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N VAL G 100 " --> pdb=" O SER G 73 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TRP G 313 " --> pdb=" O ALA G 137 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 267 through 270 removed outlier: 6.717A pdb=" N ILE G 277 " --> pdb=" O GLY G 305 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N PHE G 307 " --> pdb=" O ILE G 277 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 32 through 38 removed outlier: 6.408A pdb=" N GLN I 4 " --> pdb=" O PHE I 71 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N LEU I 73 " --> pdb=" O GLN I 4 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ARG I 6 " --> pdb=" O LEU I 73 " (cutoff:3.500A) removed outlier: 8.771A pdb=" N ASP I 70 " --> pdb=" O GLY I 90 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N TYR I 113 " --> pdb=" O GLY I 91 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N VAL I 93 " --> pdb=" O TYR I 113 " (cutoff:3.500A) 574 hydrogen bonds defined for protein. 1632 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: 2.49 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.44: 6108 1.44 - 1.65: 8566 1.65 - 1.86: 170 1.86 - 2.07: 0 2.07 - 2.29: 72 Bond restraints: 14916 Sorted by residual: bond pdb=" C4' TPP C 303 " pdb=" N4' TPP C 303 " ideal model delta sigma weight residual 1.337 1.452 -0.115 1.10e-02 8.26e+03 1.10e+02 bond pdb=" C4' TPP H 303 " pdb=" N4' TPP H 303 " ideal model delta sigma weight residual 1.337 1.445 -0.108 1.10e-02 8.26e+03 9.69e+01 bond pdb=" C4 TPP H 303 " pdb=" N3 TPP H 303 " ideal model delta sigma weight residual 1.394 1.315 0.079 1.00e-02 1.00e+04 6.24e+01 bond pdb=" C4 TPP C 303 " pdb=" N3 TPP C 303 " ideal model delta sigma weight residual 1.394 1.322 0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C7 TPP H 303 " pdb=" O7 TPP H 303 " ideal model delta sigma weight residual 1.449 1.383 0.066 1.10e-02 8.26e+03 3.60e+01 ... (remaining 14911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 20059 3.27 - 6.53: 91 6.53 - 9.80: 10 9.80 - 13.07: 3 13.07 - 16.34: 1 Bond angle restraints: 20164 Sorted by residual: angle pdb=" PA TPP C 303 " pdb=" O3A TPP C 303 " pdb=" PB TPP C 303 " ideal model delta sigma weight residual 139.87 123.53 16.34 1.00e+00 1.00e+00 2.67e+02 angle pdb=" PA TPP H 303 " pdb=" O3A TPP H 303 " pdb=" PB TPP H 303 " ideal model delta sigma weight residual 139.87 129.57 10.30 1.00e+00 1.00e+00 1.06e+02 angle pdb=" C7 TPP H 303 " pdb=" O7 TPP H 303 " pdb=" PA TPP H 303 " ideal model delta sigma weight residual 124.29 114.31 9.98 1.00e+00 1.00e+00 9.96e+01 angle pdb=" C5 TPP H 303 " pdb=" C6 TPP H 303 " pdb=" C7 TPP H 303 " ideal model delta sigma weight residual 113.13 105.83 7.30 1.00e+00 9.92e-01 5.29e+01 angle pdb=" C5' TPP H 303 " pdb=" C6' TPP H 303 " pdb=" N1' TPP H 303 " ideal model delta sigma weight residual 124.54 118.37 6.17 1.01e+00 9.80e-01 3.73e+01 ... (remaining 20159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 7771 17.96 - 35.93: 924 35.93 - 53.89: 228 53.89 - 71.86: 45 71.86 - 89.82: 22 Dihedral angle restraints: 8990 sinusoidal: 3640 harmonic: 5350 Sorted by residual: dihedral pdb=" CA SER A 110 " pdb=" C SER A 110 " pdb=" N THR A 111 " pdb=" CA THR A 111 " ideal model delta harmonic sigma weight residual -180.00 -133.12 -46.88 0 5.00e+00 4.00e-02 8.79e+01 dihedral pdb=" CA SER G 110 " pdb=" C SER G 110 " pdb=" N THR G 111 " pdb=" CA THR G 111 " ideal model delta harmonic sigma weight residual -180.00 -135.13 -44.87 0 5.00e+00 4.00e-02 8.05e+01 dihedral pdb=" CA CYS C 19 " pdb=" C CYS C 19 " pdb=" N TRP C 20 " pdb=" CA TRP C 20 " ideal model delta harmonic sigma weight residual 180.00 155.05 24.95 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 8987 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 1865 0.055 - 0.110: 326 0.110 - 0.164: 53 0.164 - 0.219: 1 0.219 - 0.274: 1 Chirality restraints: 2246 Sorted by residual: chirality pdb=" CB ILE A 279 " pdb=" CA ILE A 279 " pdb=" CG1 ILE A 279 " pdb=" CG2 ILE A 279 " both_signs ideal model delta sigma weight residual False 2.64 2.92 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB ILE G 279 " pdb=" CA ILE G 279 " pdb=" CG1 ILE G 279 " pdb=" CG2 ILE G 279 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CA ILE H 14 " pdb=" N ILE H 14 " pdb=" C ILE H 14 " pdb=" CB ILE H 14 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.60e-01 ... (remaining 2243 not shown) Planarity restraints: 2570 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR G 27 " 0.064 5.00e-02 4.00e+02 9.55e-02 1.46e+01 pdb=" N PRO G 28 " -0.165 5.00e-02 4.00e+02 pdb=" CA PRO G 28 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO G 28 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 68 " -0.010 2.00e-02 2.50e+03 2.00e-02 3.99e+00 pdb=" CD GLU B 68 " 0.035 2.00e-02 2.50e+03 pdb=" OE1 GLU B 68 " -0.012 2.00e-02 2.50e+03 pdb=" OE2 GLU B 68 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 68 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.08e+00 pdb=" C GLU B 68 " -0.030 2.00e-02 2.50e+03 pdb=" O GLU B 68 " 0.011 2.00e-02 2.50e+03 pdb=" N ILE B 69 " 0.010 2.00e-02 2.50e+03 ... (remaining 2567 not shown) Histogram of nonbonded interaction distances: 1.11 - 1.87: 1 1.87 - 2.63: 148 2.63 - 3.38: 18726 3.38 - 4.14: 33573 4.14 - 4.90: 64185 Nonbonded interactions: 116633 Sorted by model distance: nonbonded pdb="MG MG C 302 " pdb=" O3A TPP C 303 " model vdw 1.112 2.170 nonbonded pdb="MG MG H 302 " pdb=" O3A TPP H 303 " model vdw 1.878 2.170 nonbonded pdb=" OD1 ASN H 123 " pdb="MG MG H 302 " model vdw 2.022 2.170 nonbonded pdb=" OD1 ASP H 95 " pdb="MG MG H 302 " model vdw 2.029 2.170 nonbonded pdb=" O LEU A 272 " pdb=" OH TYR A 327 " model vdw 2.134 3.040 ... (remaining 116628 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 'G' } ncs_group { reference = chain 'B' selection = chain 'I' } ncs_group { reference = chain 'C' selection = chain 'H' } ncs_group { reference = chain 'D' selection = chain 'F' } 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=0.89 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.250 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.200 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7582 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 : 0.013 0.837 14944 Z= 1.292 Angle : 0.831 44.543 20236 Z= 0.368 Chirality : 0.043 0.274 2246 Planarity : 0.004 0.096 2570 Dihedral : 16.814 89.821 5562 Min Nonbonded Distance : 1.112 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.08 % Favored : 93.81 % Rotamer: Outliers : 0.25 % Allowed : 22.53 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.04 (0.20), residues: 1858 helix: -0.20 (0.19), residues: 762 sheet: -0.09 (0.29), residues: 376 loop : -1.43 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 208 TYR 0.012 0.001 TYR G 176 PHE 0.011 0.001 PHE H 155 TRP 0.015 0.001 TRP C 20 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00333 (14916) covalent geometry : angle 0.60083 (20164) hydrogen bonds : bond 0.16646 ( 574) hydrogen bonds : angle 6.92956 ( 1632) metal coordination : bond 0.00395 ( 24) metal coordination : angle 9.63089 ( 72) Misc. bond : bond 0.77644 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 414 time to evaluate : 0.585 Fit side-chains REVERT: D 14 VAL cc_start: 0.8762 (p) cc_final: 0.8456 (t) REVERT: A 174 HIS cc_start: 0.8845 (m170) cc_final: 0.8639 (m-70) REVERT: A 205 LYS cc_start: 0.7329 (mmtm) cc_final: 0.7091 (mmtt) REVERT: A 251 ASP cc_start: 0.7388 (m-30) cc_final: 0.7144 (m-30) REVERT: C 130 ASN cc_start: 0.8758 (m110) cc_final: 0.8280 (m110) REVERT: C 139 ASN cc_start: 0.8627 (m-40) cc_final: 0.7896 (m110) REVERT: C 185 LYS cc_start: 0.8135 (ttmt) cc_final: 0.7905 (mtpp) REVERT: C 208 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8294 (mtp85) REVERT: C 227 VAL cc_start: 0.8105 (m) cc_final: 0.7397 (p) REVERT: B 112 ILE cc_start: 0.7370 (tt) cc_final: 0.6827 (mt) REVERT: G 74 MET cc_start: 0.8416 (ptm) cc_final: 0.8196 (ppp) REVERT: G 144 GLU cc_start: 0.7608 (mp0) cc_final: 0.7175 (tp30) REVERT: G 180 GLN cc_start: 0.7984 (mt0) cc_final: 0.7496 (mp10) REVERT: G 273 GLU cc_start: 0.7730 (tp30) cc_final: 0.7408 (pm20) REVERT: H 1 MET cc_start: 0.6061 (ppp) cc_final: 0.5786 (ppp) REVERT: H 242 ASP cc_start: 0.7113 (p0) cc_final: 0.6773 (m-30) REVERT: I 5 LEU cc_start: 0.7396 (mt) cc_final: 0.7118 (mt) outliers start: 4 outliers final: 2 residues processed: 417 average time/residue: 0.6907 time to fit residues: 312.4003 Evaluate side-chains 221 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 219 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 125 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 HIS ** A 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN A 367 GLN ** C 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 113 ASN F 98 ASN G 218 ASN G 265 ASN H 122 ASN ** H 201 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 231 GLN I 81 ASN I 131 GLN I 167 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.144576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.126335 restraints weight = 16961.630| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.17 r_work: 0.3326 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3118 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3118 r_free = 0.3118 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 743 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2975 r_free = 0.2975 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 780 | |-----------------------------------------------------------------------------| r_final: 0.2975 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 14944 Z= 0.207 Angle : 0.927 50.407 20236 Z= 0.367 Chirality : 0.049 0.217 2246 Planarity : 0.005 0.040 2570 Dihedral : 6.415 71.164 2011 Min Nonbonded Distance : 1.821 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.43 % Allowed : 5.87 % Favored : 93.70 % Rotamer: Outliers : 6.28 % Allowed : 22.34 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.94 (0.19), residues: 1858 helix: 0.08 (0.19), residues: 758 sheet: -0.08 (0.29), residues: 346 loop : -1.57 (0.21), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 18 TYR 0.023 0.002 TYR G 327 PHE 0.027 0.002 PHE H 99 TRP 0.019 0.002 TRP C 20 HIS 0.006 0.001 HIS C 67 Details of bonding type rmsd covalent geometry : bond 0.00501 (14916) covalent geometry : angle 0.68651 (20164) hydrogen bonds : bond 0.04838 ( 574) hydrogen bonds : angle 4.67373 ( 1632) metal coordination : bond 0.00918 ( 24) metal coordination : angle 10.47779 ( 72) Misc. bond : bond 0.00332 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 253 time to evaluate : 0.607 Fit side-chains REVERT: D 14 VAL cc_start: 0.8795 (p) cc_final: 0.8559 (t) REVERT: D 42 ARG cc_start: 0.8336 (mmm-85) cc_final: 0.8124 (mmm-85) REVERT: D 61 GLN cc_start: 0.8577 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: D 68 ASP cc_start: 0.8732 (m-30) cc_final: 0.8496 (m-30) REVERT: D 92 SER cc_start: 0.8946 (OUTLIER) cc_final: 0.8719 (p) REVERT: A 87 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.8022 (tm-30) REVERT: A 339 GLN cc_start: 0.8713 (pt0) cc_final: 0.8390 (pt0) REVERT: C 51 ILE cc_start: 0.8442 (OUTLIER) cc_final: 0.7953 (mt) REVERT: C 97 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: C 185 LYS cc_start: 0.8330 (ttmt) cc_final: 0.8102 (mtpp) REVERT: C 208 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8267 (mtp85) REVERT: C 227 VAL cc_start: 0.8236 (m) cc_final: 0.7878 (p) REVERT: C 233 GLU cc_start: 0.7639 (tt0) cc_final: 0.7383 (mt-10) REVERT: C 250 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8594 (ttt180) REVERT: B 169 LYS cc_start: 0.7916 (tppp) cc_final: 0.7392 (ttpt) REVERT: F 14 VAL cc_start: 0.8684 (OUTLIER) cc_final: 0.8387 (t) REVERT: F 17 ASP cc_start: 0.9041 (m-30) cc_final: 0.8754 (m-30) REVERT: F 49 LYS cc_start: 0.6783 (OUTLIER) cc_final: 0.6300 (ptpp) REVERT: F 76 ARG cc_start: 0.7540 (OUTLIER) cc_final: 0.7332 (tpt170) REVERT: F 102 LEU cc_start: 0.8414 (pt) cc_final: 0.6764 (pp) REVERT: F 103 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8148 (pt) REVERT: G 34 ASP cc_start: 0.8935 (m-30) cc_final: 0.8469 (m-30) REVERT: G 87 GLU cc_start: 0.8630 (OUTLIER) cc_final: 0.8139 (tp30) REVERT: G 216 VAL cc_start: 0.8615 (OUTLIER) cc_final: 0.8394 (m) REVERT: G 261 GLN cc_start: 0.9036 (OUTLIER) cc_final: 0.8707 (mm110) REVERT: G 266 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8255 (mt-10) REVERT: G 267 ASN cc_start: 0.9055 (OUTLIER) cc_final: 0.8625 (m110) REVERT: G 278 VAL cc_start: 0.8559 (OUTLIER) cc_final: 0.7880 (t) REVERT: H 182 LYS cc_start: 0.8741 (OUTLIER) cc_final: 0.8233 (ttmm) REVERT: H 242 ASP cc_start: 0.8150 (p0) cc_final: 0.7670 (m-30) REVERT: I 96 ASP cc_start: 0.7960 (p0) cc_final: 0.7523 (p0) REVERT: I 152 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7782 (mt) outliers start: 99 outliers final: 26 residues processed: 322 average time/residue: 0.6564 time to fit residues: 230.7950 Evaluate side-chains 255 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 211 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain B residue 119 SER Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 14 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 107 ILE Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 87 GLU Chi-restraints excluded: chain G residue 216 VAL Chi-restraints excluded: chain G residue 261 GLN Chi-restraints excluded: chain G residue 265 ASN Chi-restraints excluded: chain G residue 266 GLU Chi-restraints excluded: chain G residue 267 ASN Chi-restraints excluded: chain G residue 278 VAL Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 182 LYS Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 166 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 49 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 137 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 chunk 104 optimal weight: 3.9990 chunk 164 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 GLN A 265 ASN C 70 HIS F 98 ASN G 180 GLN G 218 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.099840 restraints weight = 18438.049| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.35 r_work: 0.2919 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2811 r_free = 0.2811 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 780 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2805 r_free = 0.2805 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| r_final: 0.2805 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 14944 Z= 0.114 Angle : 0.804 44.116 20236 Z= 0.291 Chirality : 0.044 0.177 2246 Planarity : 0.004 0.040 2570 Dihedral : 5.879 69.492 2009 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.17 % Favored : 94.67 % Rotamer: Outliers : 5.65 % Allowed : 23.29 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.60 (0.20), residues: 1858 helix: 0.61 (0.20), residues: 740 sheet: -0.19 (0.29), residues: 342 loop : -1.45 (0.21), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 230 TYR 0.011 0.001 TYR A 327 PHE 0.013 0.001 PHE H 99 TRP 0.020 0.001 TRP C 20 HIS 0.002 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00258 (14916) covalent geometry : angle 0.54247 (20164) hydrogen bonds : bond 0.03712 ( 574) hydrogen bonds : angle 4.22530 ( 1632) metal coordination : bond 0.00663 ( 24) metal coordination : angle 9.97163 ( 72) Misc. bond : bond 0.00437 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 216 time to evaluate : 0.634 Fit side-chains REVERT: D 14 VAL cc_start: 0.8674 (p) cc_final: 0.8352 (t) REVERT: D 101 MET cc_start: 0.8397 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: A 270 MET cc_start: 0.8270 (ptm) cc_final: 0.7774 (ppp) REVERT: A 297 HIS cc_start: 0.7180 (t-170) cc_final: 0.6925 (t70) REVERT: A 339 GLN cc_start: 0.8596 (pt0) cc_final: 0.8251 (pt0) REVERT: C 51 ILE cc_start: 0.8317 (tt) cc_final: 0.8109 (mt) REVERT: C 185 LYS cc_start: 0.8340 (ttmt) cc_final: 0.8075 (mtpp) REVERT: C 197 ASP cc_start: 0.9074 (t0) cc_final: 0.8140 (t0) REVERT: C 208 ARG cc_start: 0.8624 (ttp80) cc_final: 0.8160 (mtp85) REVERT: C 227 VAL cc_start: 0.7896 (m) cc_final: 0.7644 (p) REVERT: C 250 ARG cc_start: 0.9008 (OUTLIER) cc_final: 0.8605 (ttt180) REVERT: B 169 LYS cc_start: 0.7807 (tppp) cc_final: 0.7221 (ttpt) REVERT: F 17 ASP cc_start: 0.9018 (m-30) cc_final: 0.8726 (m-30) REVERT: F 76 ARG cc_start: 0.7588 (OUTLIER) cc_final: 0.7110 (tpp-160) REVERT: F 102 LEU cc_start: 0.8292 (pt) cc_final: 0.6750 (pp) REVERT: G 273 GLU cc_start: 0.8115 (pm20) cc_final: 0.7898 (pm20) REVERT: G 278 VAL cc_start: 0.8406 (m) cc_final: 0.7542 (t) REVERT: H 179 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8437 (mtpt) REVERT: H 242 ASP cc_start: 0.8134 (p0) cc_final: 0.7702 (m-30) REVERT: I 72 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8040 (ttt) REVERT: I 152 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7614 (mt) outliers start: 89 outliers final: 30 residues processed: 283 average time/residue: 0.6965 time to fit residues: 214.8172 Evaluate side-chains 236 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 201 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 101 MET Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 351 LYS Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 53 CYS Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 85 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 98 optimal weight: 0.1980 chunk 80 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 173 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 112 optimal weight: 7.9990 chunk 183 optimal weight: 8.9990 chunk 179 optimal weight: 4.9990 chunk 103 optimal weight: 0.6980 chunk 165 optimal weight: 0.8980 chunk 149 optimal weight: 7.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN F 98 ASN G 180 GLN H 122 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.133479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.112590 restraints weight = 17699.150| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.30 r_work: 0.2917 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2825 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2845 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2845 r_free = 0.2845 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 789 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 797 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 14944 Z= 0.098 Angle : 0.788 46.138 20236 Z= 0.277 Chirality : 0.043 0.225 2246 Planarity : 0.004 0.036 2570 Dihedral : 5.640 66.947 2009 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.95 % Favored : 94.94 % Rotamer: Outliers : 4.95 % Allowed : 24.30 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.33 (0.20), residues: 1858 helix: 0.78 (0.20), residues: 752 sheet: -0.11 (0.28), residues: 364 loop : -1.27 (0.23), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 230 TYR 0.011 0.001 TYR A 176 PHE 0.010 0.001 PHE H 99 TRP 0.017 0.001 TRP C 20 HIS 0.002 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00217 (14916) covalent geometry : angle 0.52441 (20164) hydrogen bonds : bond 0.03159 ( 574) hydrogen bonds : angle 4.01031 ( 1632) metal coordination : bond 0.00548 ( 24) metal coordination : angle 9.86815 ( 72) Misc. bond : bond 0.00304 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 219 time to evaluate : 0.625 Fit side-chains revert: symmetry clash REVERT: D 14 VAL cc_start: 0.8649 (p) cc_final: 0.8275 (t) REVERT: A 267 ASN cc_start: 0.8695 (OUTLIER) cc_final: 0.8471 (m-40) REVERT: A 270 MET cc_start: 0.8275 (ptm) cc_final: 0.8006 (ptp) REVERT: A 339 GLN cc_start: 0.8619 (pt0) cc_final: 0.8083 (mt0) REVERT: C 9 LEU cc_start: 0.8757 (mt) cc_final: 0.8123 (tp) REVERT: C 17 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7748 (tt) REVERT: C 24 ASP cc_start: 0.9071 (m-30) cc_final: 0.8577 (m-30) REVERT: C 185 LYS cc_start: 0.8339 (ttmt) cc_final: 0.8072 (mtpp) REVERT: C 197 ASP cc_start: 0.9011 (t0) cc_final: 0.8049 (t0) REVERT: C 208 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8150 (mtp85) REVERT: C 227 VAL cc_start: 0.7914 (m) cc_final: 0.7713 (p) REVERT: C 250 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8625 (ttt180) REVERT: B 169 LYS cc_start: 0.7810 (tppp) cc_final: 0.7206 (ttpt) REVERT: F 17 ASP cc_start: 0.9014 (m-30) cc_final: 0.8764 (m-30) REVERT: F 76 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7119 (tpp-160) REVERT: F 94 LYS cc_start: 0.8767 (OUTLIER) cc_final: 0.8541 (mtpt) REVERT: F 102 LEU cc_start: 0.8168 (pt) cc_final: 0.6592 (pp) REVERT: F 103 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8150 (pt) REVERT: G 198 VAL cc_start: 0.8290 (t) cc_final: 0.8048 (m) REVERT: G 278 VAL cc_start: 0.8313 (m) cc_final: 0.7364 (t) REVERT: H 1 MET cc_start: 0.7520 (ppp) cc_final: 0.7229 (ppp) REVERT: H 242 ASP cc_start: 0.8152 (p0) cc_final: 0.7724 (m-30) REVERT: I 72 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7943 (ttt) REVERT: I 152 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7663 (mt) outliers start: 78 outliers final: 34 residues processed: 277 average time/residue: 0.6588 time to fit residues: 199.8696 Evaluate side-chains 246 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 204 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 372 LEU Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 94 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 155 PHE Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 16 optimal weight: 2.9990 chunk 148 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 chunk 159 optimal weight: 0.6980 chunk 57 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 112 optimal weight: 0.5980 chunk 86 optimal weight: 0.0070 chunk 15 optimal weight: 0.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 98 ASN G 180 GLN G 255 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.128303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.107517 restraints weight = 17932.162| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.29 r_work: 0.3000 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2869 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2869 r_free = 0.2869 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 797 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 801 | |-----------------------------------------------------------------------------| r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 14944 Z= 0.096 Angle : 0.786 48.628 20236 Z= 0.274 Chirality : 0.043 0.193 2246 Planarity : 0.004 0.037 2570 Dihedral : 5.416 66.317 2008 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.68 % Favored : 95.21 % Rotamer: Outliers : 4.51 % Allowed : 24.37 % Favored : 71.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.20), residues: 1858 helix: 1.02 (0.20), residues: 740 sheet: -0.09 (0.28), residues: 364 loop : -1.21 (0.22), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 230 TYR 0.012 0.001 TYR I 113 PHE 0.010 0.001 PHE H 99 TRP 0.016 0.001 TRP C 20 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00211 (14916) covalent geometry : angle 0.51419 (20164) hydrogen bonds : bond 0.03070 ( 574) hydrogen bonds : angle 3.92550 ( 1632) metal coordination : bond 0.00534 ( 24) metal coordination : angle 9.98888 ( 72) Misc. bond : bond 0.00292 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 209 time to evaluate : 0.626 Fit side-chains revert: symmetry clash REVERT: D 14 VAL cc_start: 0.8682 (p) cc_final: 0.8292 (t) REVERT: D 61 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.7930 (mp10) REVERT: A 179 VAL cc_start: 0.9068 (OUTLIER) cc_final: 0.8833 (p) REVERT: A 267 ASN cc_start: 0.8784 (OUTLIER) cc_final: 0.8581 (m-40) REVERT: A 270 MET cc_start: 0.8330 (ptm) cc_final: 0.8082 (ptp) REVERT: A 339 GLN cc_start: 0.8665 (pt0) cc_final: 0.8119 (mt0) REVERT: C 9 LEU cc_start: 0.8789 (mt) cc_final: 0.8163 (tp) REVERT: C 17 LEU cc_start: 0.7891 (OUTLIER) cc_final: 0.7597 (tt) REVERT: C 185 LYS cc_start: 0.8321 (ttmt) cc_final: 0.8061 (mtpp) REVERT: C 208 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8197 (mtp85) REVERT: C 227 VAL cc_start: 0.7986 (m) cc_final: 0.7766 (p) REVERT: C 250 ARG cc_start: 0.9011 (OUTLIER) cc_final: 0.8655 (ttt180) REVERT: B 2 GLU cc_start: 0.5790 (OUTLIER) cc_final: 0.5473 (tm-30) REVERT: B 169 LYS cc_start: 0.7873 (tppp) cc_final: 0.7235 (ttpt) REVERT: F 17 ASP cc_start: 0.9048 (m-30) cc_final: 0.8802 (m-30) REVERT: F 49 LYS cc_start: 0.6498 (OUTLIER) cc_final: 0.5228 (ptpp) REVERT: F 76 ARG cc_start: 0.7570 (OUTLIER) cc_final: 0.7145 (tpp-160) REVERT: F 103 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8159 (pt) REVERT: G 174 HIS cc_start: 0.8900 (m170) cc_final: 0.8444 (m-70) REVERT: G 189 LYS cc_start: 0.8820 (mtmm) cc_final: 0.8390 (mtmm) REVERT: G 198 VAL cc_start: 0.8361 (t) cc_final: 0.8131 (m) REVERT: H 1 MET cc_start: 0.7510 (ppp) cc_final: 0.7267 (ppp) REVERT: H 242 ASP cc_start: 0.8129 (p0) cc_final: 0.7670 (m-30) REVERT: I 72 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.7896 (ttt) REVERT: I 152 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7673 (mt) outliers start: 71 outliers final: 31 residues processed: 260 average time/residue: 0.6594 time to fit residues: 187.0001 Evaluate side-chains 250 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain B residue 2 GLU Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 155 PHE Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 150 ILE Chi-restraints excluded: chain I residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 10 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.0770 chunk 180 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 156 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN F 98 ASN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.101612 restraints weight = 18201.050| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.33 r_work: 0.2995 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2904 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 801 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 809 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.5002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 14944 Z= 0.099 Angle : 0.792 50.529 20236 Z= 0.273 Chirality : 0.043 0.189 2246 Planarity : 0.004 0.038 2570 Dihedral : 5.374 65.059 2008 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.79 % Favored : 95.10 % Rotamer: Outliers : 4.70 % Allowed : 24.43 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.20), residues: 1858 helix: 0.99 (0.20), residues: 752 sheet: -0.02 (0.29), residues: 358 loop : -1.14 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 230 TYR 0.012 0.001 TYR A 176 PHE 0.012 0.001 PHE H 99 TRP 0.015 0.001 TRP C 20 HIS 0.008 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00224 (14916) covalent geometry : angle 0.51431 (20164) hydrogen bonds : bond 0.03185 ( 574) hydrogen bonds : angle 3.90881 ( 1632) metal coordination : bond 0.00555 ( 24) metal coordination : angle 10.11718 ( 72) Misc. bond : bond 0.00328 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 208 time to evaluate : 0.592 Fit side-chains REVERT: D 14 VAL cc_start: 0.8755 (p) cc_final: 0.8366 (t) REVERT: D 61 GLN cc_start: 0.8713 (OUTLIER) cc_final: 0.8120 (mp10) REVERT: A 179 VAL cc_start: 0.9102 (OUTLIER) cc_final: 0.8889 (p) REVERT: A 270 MET cc_start: 0.8372 (ptm) cc_final: 0.7894 (ppp) REVERT: A 339 GLN cc_start: 0.8727 (pt0) cc_final: 0.8126 (mt0) REVERT: C 9 LEU cc_start: 0.8855 (mt) cc_final: 0.8242 (tp) REVERT: C 17 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7609 (tt) REVERT: C 185 LYS cc_start: 0.8332 (ttmt) cc_final: 0.8078 (mtpp) REVERT: C 197 ASP cc_start: 0.8992 (t0) cc_final: 0.8018 (t0) REVERT: C 208 ARG cc_start: 0.8698 (ttp80) cc_final: 0.8178 (mtp180) REVERT: C 227 VAL cc_start: 0.8089 (m) cc_final: 0.7856 (p) REVERT: C 239 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7898 (mp0) REVERT: C 250 ARG cc_start: 0.9036 (OUTLIER) cc_final: 0.8698 (ttt180) REVERT: B 169 LYS cc_start: 0.8001 (tppp) cc_final: 0.7368 (ttpt) REVERT: F 17 ASP cc_start: 0.9070 (m-30) cc_final: 0.8838 (m-30) REVERT: F 49 LYS cc_start: 0.6588 (OUTLIER) cc_final: 0.5289 (ptpp) REVERT: F 76 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7224 (tpp-160) REVERT: F 103 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8263 (pt) REVERT: G 174 HIS cc_start: 0.8945 (m170) cc_final: 0.8479 (m-70) REVERT: G 189 LYS cc_start: 0.8771 (mtmm) cc_final: 0.8445 (mtmm) REVERT: G 198 VAL cc_start: 0.8410 (t) cc_final: 0.8203 (m) REVERT: H 242 ASP cc_start: 0.8173 (p0) cc_final: 0.7706 (m-30) REVERT: I 72 MET cc_start: 0.8745 (OUTLIER) cc_final: 0.7952 (ttt) REVERT: I 152 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7731 (mt) outliers start: 74 outliers final: 37 residues processed: 257 average time/residue: 0.6287 time to fit residues: 176.6887 Evaluate side-chains 251 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 262 ASP Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 97 ASP Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 270 MET Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 155 PHE Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 125 optimal weight: 0.6980 chunk 145 optimal weight: 6.9990 chunk 178 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN F 98 ASN G 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.116552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.095538 restraints weight = 18366.166| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 1.26 r_work: 0.2873 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2761 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2761 r_free = 0.2761 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 809 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 806 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.5247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 14944 Z= 0.164 Angle : 0.878 49.871 20236 Z= 0.324 Chirality : 0.047 0.193 2246 Planarity : 0.004 0.043 2570 Dihedral : 5.749 65.809 2008 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.60 % Favored : 94.03 % Rotamer: Outliers : 5.08 % Allowed : 23.86 % Favored : 71.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.20), residues: 1858 helix: 0.72 (0.20), residues: 756 sheet: 0.07 (0.28), residues: 356 loop : -1.31 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 230 TYR 0.014 0.001 TYR I 113 PHE 0.019 0.002 PHE H 99 TRP 0.015 0.002 TRP H 20 HIS 0.009 0.001 HIS A 297 Details of bonding type rmsd covalent geometry : bond 0.00403 (14916) covalent geometry : angle 0.60804 (20164) hydrogen bonds : bond 0.04456 ( 574) hydrogen bonds : angle 4.22727 ( 1632) metal coordination : bond 0.00901 ( 24) metal coordination : angle 10.62703 ( 72) Misc. bond : bond 0.00556 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 197 time to evaluate : 0.521 Fit side-chains REVERT: D 14 VAL cc_start: 0.8735 (p) cc_final: 0.8367 (t) REVERT: D 61 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8123 (mp10) REVERT: A 179 VAL cc_start: 0.9143 (OUTLIER) cc_final: 0.8906 (p) REVERT: A 200 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8028 (m-30) REVERT: A 267 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8497 (m110) REVERT: A 270 MET cc_start: 0.8337 (ptm) cc_final: 0.7812 (ppp) REVERT: A 339 GLN cc_start: 0.8719 (pt0) cc_final: 0.8362 (pt0) REVERT: C 185 LYS cc_start: 0.8366 (ttmt) cc_final: 0.8084 (mtpp) REVERT: C 227 VAL cc_start: 0.8108 (m) cc_final: 0.7857 (p) REVERT: C 250 ARG cc_start: 0.9020 (OUTLIER) cc_final: 0.8662 (ttt180) REVERT: F 49 LYS cc_start: 0.6853 (OUTLIER) cc_final: 0.5525 (ptpp) REVERT: F 76 ARG cc_start: 0.7616 (OUTLIER) cc_final: 0.7208 (tpp-160) REVERT: F 102 LEU cc_start: 0.8326 (pt) cc_final: 0.6708 (pp) REVERT: F 103 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8237 (pt) REVERT: G 189 LYS cc_start: 0.8723 (mtmm) cc_final: 0.8401 (mtmm) REVERT: G 198 VAL cc_start: 0.8445 (t) cc_final: 0.8229 (m) REVERT: G 280 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7538 (mt) REVERT: H 242 ASP cc_start: 0.8141 (p0) cc_final: 0.7690 (m-30) REVERT: I 72 MET cc_start: 0.8841 (OUTLIER) cc_final: 0.7905 (ttt) REVERT: I 152 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7662 (mt) REVERT: I 156 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.6025 (mp) outliers start: 80 outliers final: 36 residues processed: 256 average time/residue: 0.6563 time to fit residues: 183.6678 Evaluate side-chains 238 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 190 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 158 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 200 ASP Chi-restraints excluded: chain A residue 267 ASN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 155 PHE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 270 MET Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 228 SER Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 156 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 150 optimal weight: 0.9980 chunk 82 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 147 optimal weight: 0.1980 chunk 133 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 131 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 180 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.131318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.112791 restraints weight = 17446.260| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 1.20 r_work: 0.2943 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 806 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2836 r_free = 0.2836 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 815 | |-----------------------------------------------------------------------------| r_final: 0.2836 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.5283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14944 Z= 0.105 Angle : 0.810 49.009 20236 Z= 0.286 Chirality : 0.044 0.183 2246 Planarity : 0.004 0.049 2570 Dihedral : 5.487 62.003 2008 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.27 % Favored : 94.56 % Rotamer: Outliers : 3.62 % Allowed : 26.46 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1858 helix: 0.90 (0.20), residues: 754 sheet: 0.04 (0.29), residues: 338 loop : -1.23 (0.22), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG H 230 TYR 0.012 0.001 TYR A 176 PHE 0.011 0.001 PHE H 99 TRP 0.019 0.001 TRP C 20 HIS 0.003 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00240 (14916) covalent geometry : angle 0.53800 (20164) hydrogen bonds : bond 0.03307 ( 574) hydrogen bonds : angle 4.00940 ( 1632) metal coordination : bond 0.00567 ( 24) metal coordination : angle 10.16050 ( 72) Misc. bond : bond 0.00312 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 201 time to evaluate : 0.536 Fit side-chains REVERT: D 14 VAL cc_start: 0.8757 (OUTLIER) cc_final: 0.8399 (t) REVERT: D 61 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.8162 (mp10) REVERT: A 87 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8277 (tm-30) REVERT: A 179 VAL cc_start: 0.9160 (OUTLIER) cc_final: 0.8941 (p) REVERT: A 270 MET cc_start: 0.8360 (ptm) cc_final: 0.7916 (ppp) REVERT: A 339 GLN cc_start: 0.8676 (pt0) cc_final: 0.8105 (mt0) REVERT: C 17 LEU cc_start: 0.8165 (tp) cc_final: 0.7703 (tt) REVERT: C 185 LYS cc_start: 0.8359 (ttmt) cc_final: 0.8086 (mtpp) REVERT: C 197 ASP cc_start: 0.9014 (t0) cc_final: 0.8119 (t0) REVERT: C 208 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8076 (mtp180) REVERT: C 227 VAL cc_start: 0.8163 (m) cc_final: 0.7957 (p) REVERT: C 250 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8673 (ttt180) REVERT: F 49 LYS cc_start: 0.6606 (OUTLIER) cc_final: 0.5319 (ptpp) REVERT: F 76 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7251 (tpp-160) REVERT: F 102 LEU cc_start: 0.8182 (pt) cc_final: 0.6613 (pp) REVERT: F 103 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8322 (pt) REVERT: G 189 LYS cc_start: 0.8647 (mtmm) cc_final: 0.8401 (mtmm) REVERT: G 198 VAL cc_start: 0.8434 (t) cc_final: 0.8223 (m) REVERT: H 242 ASP cc_start: 0.8050 (p0) cc_final: 0.7597 (m-30) REVERT: I 72 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8004 (ttt) REVERT: I 86 ASP cc_start: 0.8816 (m-30) cc_final: 0.8306 (m-30) REVERT: I 152 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7754 (mt) REVERT: I 156 LEU cc_start: 0.7456 (mt) cc_final: 0.6074 (mp) outliers start: 57 outliers final: 34 residues processed: 242 average time/residue: 0.6656 time to fit residues: 175.8407 Evaluate side-chains 240 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 270 MET Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 155 PHE Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 85 optimal weight: 0.0030 chunk 46 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 141 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.0994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN G 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.128127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.108319 restraints weight = 17586.858| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.32 r_work: 0.2967 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 815 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2857 r_free = 0.2857 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 816 | |-----------------------------------------------------------------------------| r_final: 0.2857 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 14944 Z= 0.122 Angle : 0.833 51.011 20236 Z= 0.296 Chirality : 0.045 0.182 2246 Planarity : 0.004 0.041 2570 Dihedral : 5.548 62.685 2008 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.87 % Favored : 93.92 % Rotamer: Outliers : 3.43 % Allowed : 26.33 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.20), residues: 1858 helix: 0.90 (0.20), residues: 754 sheet: 0.16 (0.30), residues: 330 loop : -1.29 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 230 TYR 0.015 0.001 TYR I 113 PHE 0.015 0.001 PHE H 99 TRP 0.016 0.001 TRP C 20 HIS 0.003 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00290 (14916) covalent geometry : angle 0.55644 (20164) hydrogen bonds : bond 0.03662 ( 574) hydrogen bonds : angle 4.04830 ( 1632) metal coordination : bond 0.00662 ( 24) metal coordination : angle 10.41228 ( 72) Misc. bond : bond 0.00398 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 198 time to evaluate : 0.517 Fit side-chains REVERT: D 14 VAL cc_start: 0.8754 (OUTLIER) cc_final: 0.8400 (t) REVERT: D 61 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8178 (mp10) REVERT: A 87 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8306 (tm-30) REVERT: A 179 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8913 (p) REVERT: A 339 GLN cc_start: 0.8707 (pt0) cc_final: 0.8099 (mt0) REVERT: C 17 LEU cc_start: 0.8211 (tp) cc_final: 0.7801 (tt) REVERT: C 24 ASP cc_start: 0.9092 (m-30) cc_final: 0.8219 (m-30) REVERT: C 44 ASP cc_start: 0.8302 (m-30) cc_final: 0.8057 (m-30) REVERT: C 185 LYS cc_start: 0.8343 (ttmt) cc_final: 0.8063 (mtpp) REVERT: C 197 ASP cc_start: 0.9026 (t0) cc_final: 0.8152 (t0) REVERT: C 208 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8051 (mtp180) REVERT: C 227 VAL cc_start: 0.8154 (m) cc_final: 0.7942 (p) REVERT: C 250 ARG cc_start: 0.9042 (OUTLIER) cc_final: 0.8681 (ttt180) REVERT: F 49 LYS cc_start: 0.6771 (OUTLIER) cc_final: 0.5533 (ptpp) REVERT: F 76 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7310 (tpp-160) REVERT: F 102 LEU cc_start: 0.8251 (pt) cc_final: 0.6694 (pp) REVERT: F 103 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8257 (pt) REVERT: G 189 LYS cc_start: 0.8658 (mtmm) cc_final: 0.8401 (mtmm) REVERT: G 198 VAL cc_start: 0.8426 (t) cc_final: 0.8206 (m) REVERT: I 72 MET cc_start: 0.8855 (OUTLIER) cc_final: 0.7990 (ttt) REVERT: I 152 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7705 (mt) REVERT: I 156 LEU cc_start: 0.7370 (OUTLIER) cc_final: 0.5951 (mp) outliers start: 54 outliers final: 37 residues processed: 235 average time/residue: 0.6682 time to fit residues: 171.5532 Evaluate side-chains 243 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 195 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 61 GLN Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 270 MET Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 155 PHE Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 LEU Chi-restraints excluded: chain I residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 167 optimal weight: 5.9990 chunk 141 optimal weight: 0.7980 chunk 181 optimal weight: 6.9990 chunk 110 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.124178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.103672 restraints weight = 17557.256| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 1.27 r_work: 0.3025 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2788 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2788 r_free = 0.2788 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 816 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2786 r_free = 0.2786 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 821 | |-----------------------------------------------------------------------------| r_final: 0.2786 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 14944 Z= 0.177 Angle : 0.891 49.871 20236 Z= 0.334 Chirality : 0.047 0.204 2246 Planarity : 0.004 0.045 2570 Dihedral : 5.853 64.599 2008 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.97 % Favored : 93.65 % Rotamer: Outliers : 3.74 % Allowed : 26.08 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.20), residues: 1858 helix: 0.66 (0.20), residues: 760 sheet: -0.05 (0.29), residues: 330 loop : -1.34 (0.21), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 230 TYR 0.017 0.001 TYR A 327 PHE 0.019 0.002 PHE H 99 TRP 0.018 0.002 TRP H 20 HIS 0.005 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00439 (14916) covalent geometry : angle 0.62746 (20164) hydrogen bonds : bond 0.04555 ( 574) hydrogen bonds : angle 4.25734 ( 1632) metal coordination : bond 0.00978 ( 24) metal coordination : angle 10.61751 ( 72) Misc. bond : bond 0.00584 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3716 Ramachandran restraints generated. 1858 Oldfield, 0 Emsley, 1858 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 191 time to evaluate : 0.560 Fit side-chains REVERT: D 14 VAL cc_start: 0.8810 (OUTLIER) cc_final: 0.8461 (t) REVERT: D 41 GLU cc_start: 0.8505 (OUTLIER) cc_final: 0.8289 (mm-30) REVERT: A 87 GLU cc_start: 0.8585 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: A 339 GLN cc_start: 0.8799 (pt0) cc_final: 0.8460 (pt0) REVERT: C 44 ASP cc_start: 0.8357 (m-30) cc_final: 0.8135 (m-30) REVERT: C 185 LYS cc_start: 0.8403 (ttmt) cc_final: 0.8112 (mtpp) REVERT: C 197 ASP cc_start: 0.9042 (t0) cc_final: 0.8304 (t0) REVERT: C 208 ARG cc_start: 0.8681 (ttp80) cc_final: 0.8118 (mtp85) REVERT: C 227 VAL cc_start: 0.8224 (m) cc_final: 0.7973 (p) REVERT: C 230 ARG cc_start: 0.8015 (ttt90) cc_final: 0.7613 (ttp80) REVERT: C 233 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7536 (mt-10) REVERT: C 250 ARG cc_start: 0.9106 (OUTLIER) cc_final: 0.8731 (ttt180) REVERT: F 49 LYS cc_start: 0.6874 (OUTLIER) cc_final: 0.5575 (ptpp) REVERT: F 76 ARG cc_start: 0.7734 (OUTLIER) cc_final: 0.7528 (tpp-160) REVERT: F 102 LEU cc_start: 0.8407 (pt) cc_final: 0.6737 (pp) REVERT: F 103 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8312 (pt) REVERT: G 189 LYS cc_start: 0.8726 (mtmm) cc_final: 0.8468 (mtmm) REVERT: G 198 VAL cc_start: 0.8457 (t) cc_final: 0.8240 (m) REVERT: I 72 MET cc_start: 0.8891 (OUTLIER) cc_final: 0.8023 (ttt) REVERT: I 152 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7738 (mt) REVERT: I 156 LEU cc_start: 0.7384 (mt) cc_final: 0.5956 (mp) outliers start: 59 outliers final: 43 residues processed: 233 average time/residue: 0.6590 time to fit residues: 168.0408 Evaluate side-chains 239 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 187 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 41 GLU Chi-restraints excluded: chain D residue 44 LEU Chi-restraints excluded: chain D residue 92 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 87 GLU Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain C residue 3 PHE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 125 ILE Chi-restraints excluded: chain C residue 224 SER Chi-restraints excluded: chain C residue 250 ARG Chi-restraints excluded: chain C residue 253 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 41 SER Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 42 ARG Chi-restraints excluded: chain F residue 49 LYS Chi-restraints excluded: chain F residue 76 ARG Chi-restraints excluded: chain F residue 84 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain G residue 30 THR Chi-restraints excluded: chain G residue 68 MET Chi-restraints excluded: chain G residue 270 MET Chi-restraints excluded: chain G residue 280 ILE Chi-restraints excluded: chain G residue 362 THR Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 53 CYS Chi-restraints excluded: chain H residue 61 VAL Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 97 ASP Chi-restraints excluded: chain H residue 129 THR Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 246 THR Chi-restraints excluded: chain I residue 10 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 72 MET Chi-restraints excluded: chain I residue 96 ASP Chi-restraints excluded: chain I residue 129 ILE Chi-restraints excluded: chain I residue 146 VAL Chi-restraints excluded: chain I residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 184 random chunks: chunk 99 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 175 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 154 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN ** G 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.128260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.108589 restraints weight = 17283.291| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.30 r_work: 0.3083 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2913 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2913 r_free = 0.2913 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 821 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2911 r_free = 0.2911 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 823 | |-----------------------------------------------------------------------------| r_final: 0.2911 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.5538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14944 Z= 0.137 Angle : 0.854 49.357 20236 Z= 0.311 Chirality : 0.046 0.187 2246 Planarity : 0.004 0.042 2570 Dihedral : 5.758 63.087 2008 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.60 % Favored : 94.13 % Rotamer: Outliers : 3.43 % Allowed : 26.40 % Favored : 70.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.20), residues: 1858 helix: 0.73 (0.20), residues: 758 sheet: 0.09 (0.30), residues: 330 loop : -1.38 (0.21), residues: 770 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 230 TYR 0.015 0.001 TYR A 327 PHE 0.017 0.001 PHE H 99 TRP 0.017 0.002 TRP C 20 HIS 0.004 0.001 HIS A 227 Details of bonding type rmsd covalent geometry : bond 0.00331 (14916) covalent geometry : angle 0.58535 (20164) hydrogen bonds : bond 0.03949 ( 574) hydrogen bonds : angle 4.16580 ( 1632) metal coordination : bond 0.00784 ( 24) metal coordination : angle 10.45151 ( 72) Misc. bond : bond 0.00435 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5401.98 seconds wall clock time: 92 minutes 48.63 seconds (5568.63 seconds total)