Starting phenix.real_space_refine on Fri Dec 15 06:53:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1w_15091/12_2023/8a1w_15091_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1w_15091/12_2023/8a1w_15091.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1w_15091/12_2023/8a1w_15091.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1w_15091/12_2023/8a1w_15091.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1w_15091/12_2023/8a1w_15091_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a1w_15091/12_2023/8a1w_15091_trim_updated.pdb" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Fe 4 7.16 5 P 8 5.49 5 S 90 5.16 5 Na 2 4.78 5 C 9803 2.51 5 N 2437 2.21 5 O 3052 1.98 5 H 14776 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 131": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 28": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 30172 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 6877 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 422} Chain: "B" Number of atoms: 6346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 412, 6346 Classifications: {'peptide': 412} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 395} Chain: "C" Number of atoms: 3774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 3774 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 7, 'TRANS': 240} Chain: "D" Number of atoms: 3154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3154 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 9, 'TRANS': 191} Chain: "E" Number of atoms: 3041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 3041 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain: "F" Number of atoms: 6239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 406, 6239 Classifications: {'peptide': 406} Link IDs: {'PTRANS': 24, 'TRANS': 381} Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 282 Unusual residues: {' NA': 2, '3PE': 3, 'FMN': 1, 'LMT': 2, 'RBF': 1, 'UQ1': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 18 Chain: "C" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'FMN': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Chain: "D" Number of atoms: 79 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 79 Unusual residues: {'3PE': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "E" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 57 Unusual residues: {'FAD': 1, 'FES': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 145 Classifications: {'water': 145} Link IDs: {None: 144} Chain: "B" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 117 Classifications: {'water': 117} Link IDs: {None: 116} Chain: "C" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "D" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "E" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 18661 SG CYS D 112 67.213 82.111 58.874 1.00 24.95 S ATOM 20553 SG CYS E 26 64.800 82.618 61.643 1.00 5.84 S ATOM 17328 SG CYS D 29 67.684 83.714 65.347 1.00 23.84 S ATOM 22058 SG CYS E 120 70.535 84.585 62.993 1.00 23.62 S ATOM 24222 SG CYS F 70 53.201 67.528 38.642 1.00 11.37 S ATOM 24271 SG CYS F 76 51.055 64.749 37.261 1.00 12.01 S ATOM 24305 SG CYS F 79 55.886 61.678 37.911 1.00 16.45 S ATOM 24789 SG CYS F 111 57.219 64.963 39.196 1.00 14.30 S Time building chain proxies: 12.95, per 1000 atoms: 0.43 Number of scatterers: 30172 At special positions: 0 Unit cell: (113.15, 135.05, 131.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Fe 4 26.01 S 90 16.00 P 8 15.00 Na 2 11.00 O 3052 8.00 N 2437 7.00 C 9803 6.00 H 14776 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 27.69 Conformation dependent library (CDL) restraints added in 3.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES E1001 " pdb="FE1 FES E1001 " - pdb=" SG CYS E 26 " pdb="FE1 FES E1001 " - pdb=" SG CYS D 112 " pdb="FE2 FES E1001 " - pdb=" SG CYS D 29 " pdb="FE2 FES E1001 " - pdb=" SG CYS E 120 " pdb=" FES F1502 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 76 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 111 " pdb="FE2 FES F1502 " - pdb=" SG CYS F 79 " pdb="FE1 FES F1502 " - pdb=" SG CYS F 70 " Number of angles added : 12 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3448 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 85 helices and 14 sheets defined 47.2% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.50 Creating SS restraints... Processing helix chain 'A' and resid 33 through 35 No H-bonds generated for 'chain 'A' and resid 33 through 35' Processing helix chain 'A' and resid 83 through 85 No H-bonds generated for 'chain 'A' and resid 83 through 85' Processing helix chain 'A' and resid 107 through 112 removed outlier: 3.578A pdb=" N LEU A 110 " --> pdb=" O ALA A 107 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N ALA A 111 " --> pdb=" O ASN A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 125 Processing helix chain 'A' and resid 127 through 130 Processing helix chain 'A' and resid 163 through 184 removed outlier: 3.720A pdb=" N GLU A 169 " --> pdb=" O VAL A 165 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLN A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N GLU A 172 " --> pdb=" O ASN A 168 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA A 173 " --> pdb=" O GLU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 283 through 286 No H-bonds generated for 'chain 'A' and resid 283 through 286' Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 336 through 338 No H-bonds generated for 'chain 'A' and resid 336 through 338' Processing helix chain 'A' and resid 352 through 355 Processing helix chain 'A' and resid 379 through 382 No H-bonds generated for 'chain 'A' and resid 379 through 382' Processing helix chain 'A' and resid 390 through 399 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 410 through 412 No H-bonds generated for 'chain 'A' and resid 410 through 412' Processing helix chain 'A' and resid 415 through 423 removed outlier: 5.067A pdb=" N LEU A 420 " --> pdb=" O ASP A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 445 Processing helix chain 'B' and resid 4 through 14 removed outlier: 4.538A pdb=" N HIS B 12 " --> pdb=" O GLU B 8 " (cutoff:3.500A) removed outlier: 4.908A pdb=" N HIS B 13 " --> pdb=" O ASP B 9 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N PHE B 14 " --> pdb=" O ILE B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 34 removed outlier: 4.805A pdb=" N ALA B 25 " --> pdb=" O LYS B 22 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N GLU B 28 " --> pdb=" O ALA B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 53 through 63 Processing helix chain 'B' and resid 65 through 86 Processing helix chain 'B' and resid 90 through 97 Processing helix chain 'B' and resid 100 through 107 removed outlier: 3.537A pdb=" N THR B 105 " --> pdb=" O HIS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 151 removed outlier: 3.661A pdb=" N TYR B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Proline residue: B 131 - end of helix Processing helix chain 'B' and resid 157 through 168 removed outlier: 3.670A pdb=" N SER B 163 " --> pdb=" O PHE B 160 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU B 165 " --> pdb=" O THR B 162 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE B 166 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 Processing helix chain 'B' and resid 192 through 194 No H-bonds generated for 'chain 'B' and resid 192 through 194' Processing helix chain 'B' and resid 204 through 215 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 237 through 248 removed outlier: 8.631A pdb=" N ALA B 246 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA B 248 " --> pdb=" O GLY B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 277 through 289 Processing helix chain 'B' and resid 295 through 315 Processing helix chain 'B' and resid 321 through 324 Processing helix chain 'B' and resid 327 through 331 Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 354 through 374 Processing helix chain 'B' and resid 382 through 409 removed outlier: 3.706A pdb=" N PHE B 392 " --> pdb=" O PHE B 388 " (cutoff:3.500A) Proline residue: B 394 - end of helix Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 8 through 53 removed outlier: 4.812A pdb=" N ASP C 35 " --> pdb=" O VAL C 31 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N LYS C 36 " --> pdb=" O GLY C 32 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ASP C 44 " --> pdb=" O ASN C 40 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS C 45 " --> pdb=" O ALA C 41 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'C' and resid 93 through 98 Processing helix chain 'C' and resid 100 through 102 No H-bonds generated for 'chain 'C' and resid 100 through 102' Processing helix chain 'C' and resid 178 through 181 Processing helix chain 'C' and resid 183 through 189 removed outlier: 4.152A pdb=" N TRP C 189 " --> pdb=" O TRP C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 238 Processing helix chain 'C' and resid 245 through 252 Processing helix chain 'D' and resid 9 through 16 Proline residue: D 14 - end of helix Processing helix chain 'D' and resid 28 through 31 No H-bonds generated for 'chain 'D' and resid 28 through 31' Processing helix chain 'D' and resid 38 through 61 Processing helix chain 'D' and resid 68 through 92 removed outlier: 3.592A pdb=" N ARG D 71 " --> pdb=" O ASN D 68 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE D 72 " --> pdb=" O SER D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 101 Processing helix chain 'D' and resid 106 through 108 No H-bonds generated for 'chain 'D' and resid 106 through 108' Processing helix chain 'D' and resid 112 through 120 Processing helix chain 'D' and resid 122 through 124 No H-bonds generated for 'chain 'D' and resid 122 through 124' Processing helix chain 'D' and resid 127 through 157 Processing helix chain 'D' and resid 169 through 171 No H-bonds generated for 'chain 'D' and resid 169 through 171' Processing helix chain 'D' and resid 179 through 182 Processing helix chain 'D' and resid 184 through 201 removed outlier: 3.744A pdb=" N PHE D 188 " --> pdb=" O ALA D 184 " (cutoff:3.500A) Processing helix chain 'D' and resid 203 through 205 No H-bonds generated for 'chain 'D' and resid 203 through 205' Processing helix chain 'E' and resid 3 through 10 Processing helix chain 'E' and resid 25 through 28 No H-bonds generated for 'chain 'E' and resid 25 through 28' Processing helix chain 'E' and resid 35 through 62 Proline residue: E 54 - end of helix Processing helix chain 'E' and resid 80 through 101 Processing helix chain 'E' and resid 103 through 108 Processing helix chain 'E' and resid 110 through 116 Proline residue: E 114 - end of helix No H-bonds generated for 'chain 'E' and resid 110 through 116' Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'E' and resid 136 through 166 removed outlier: 3.572A pdb=" N LYS E 165 " --> pdb=" O ARG E 161 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N TYR E 166 " --> pdb=" O GLU E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 193 removed outlier: 4.719A pdb=" N SER E 192 " --> pdb=" O LEU E 188 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N PHE E 193 " --> pdb=" O GLY E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 3 through 29 Processing helix chain 'F' and resid 55 through 61 removed outlier: 3.526A pdb=" N ALA F 60 " --> pdb=" O LEU F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 96 removed outlier: 3.670A pdb=" N ASP F 96 " --> pdb=" O PRO F 92 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 92 through 96' Processing helix chain 'F' and resid 100 through 105 Processing helix chain 'F' and resid 125 through 128 No H-bonds generated for 'chain 'F' and resid 125 through 128' Processing helix chain 'F' and resid 179 through 181 No H-bonds generated for 'chain 'F' and resid 179 through 181' Processing helix chain 'F' and resid 186 through 194 removed outlier: 4.057A pdb=" N ASP F 191 " --> pdb=" O LYS F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 199 No H-bonds generated for 'chain 'F' and resid 197 through 199' Processing helix chain 'F' and resid 245 through 251 Processing helix chain 'F' and resid 282 through 294 Proline residue: F 287 - end of helix Processing helix chain 'F' and resid 320 through 329 Processing helix chain 'F' and resid 355 through 362 removed outlier: 4.344A pdb=" N TYR F 360 " --> pdb=" O HIS F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 381 through 394 Processing helix chain 'F' and resid 398 through 400 No H-bonds generated for 'chain 'F' and resid 398 through 400' Processing sheet with id= A, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.455A pdb=" N LEU A 274 " --> pdb=" O SER A 21 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N GLN A 322 " --> pdb=" O GLY A 301 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 28 through 32 removed outlier: 3.716A pdb=" N GLU A 78 " --> pdb=" O VAL A 91 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N GLU A 93 " --> pdb=" O VAL A 76 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N VAL A 76 " --> pdb=" O GLU A 93 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 41 through 43 removed outlier: 7.151A pdb=" N PHE A 68 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 132 through 134 removed outlier: 6.618A pdb=" N LYS A 188 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL A 151 " --> pdb=" O LYS A 188 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N TYR A 190 " --> pdb=" O VAL A 151 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 82 through 84 removed outlier: 3.558A pdb=" N ASP C 82 " --> pdb=" O ASP C 77 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LEU C 75 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 126 " --> pdb=" O GLU C 72 " (cutoff:3.500A) removed outlier: 14.212A pdb=" N VAL C 121 " --> pdb=" O HIS C 141 " (cutoff:3.500A) removed outlier: 12.321A pdb=" N HIS C 141 " --> pdb=" O VAL C 121 " (cutoff:3.500A) removed outlier: 7.420A pdb=" N VAL C 123 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE C 152 " --> pdb=" O TYR C 167 " (cutoff:3.500A) removed outlier: 5.455A pdb=" N TYR C 167 " --> pdb=" O PHE C 152 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ALA C 154 " --> pdb=" O LEU C 165 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LEU C 165 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 103 through 105 Processing sheet with id= G, first strand: chain 'C' and resid 204 through 206 Processing sheet with id= H, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= I, first strand: chain 'F' and resid 80 through 82 Processing sheet with id= J, first strand: chain 'F' and resid 134 through 136 Processing sheet with id= K, first strand: chain 'F' and resid 147 through 153 Processing sheet with id= L, first strand: chain 'F' and resid 167 through 172 Processing sheet with id= M, first strand: chain 'F' and resid 175 through 178 Processing sheet with id= N, first strand: chain 'F' and resid 401 through 403 removed outlier: 6.650A pdb=" N TYR F 375 " --> pdb=" O LEU F 402 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA F 338 " --> pdb=" O TYR F 309 " (cutoff:3.500A) 635 hydrogen bonds defined for protein. 1719 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: 11.74 Time building geometry restraints manager: 28.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 14763 1.11 - 1.38: 5837 1.38 - 1.66: 9469 1.66 - 1.93: 151 1.93 - 2.20: 8 Bond restraints: 30228 Sorted by residual: bond pdb=" N ASP A 212 " pdb=" H ASP A 212 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.86e+01 bond pdb=" N LEU A 219 " pdb=" H LEU A 219 " ideal model delta sigma weight residual 0.860 1.037 -0.177 2.00e-02 2.50e+03 7.81e+01 bond pdb=" N HIS A 215 " pdb=" H HIS A 215 " ideal model delta sigma weight residual 0.860 1.036 -0.176 2.00e-02 2.50e+03 7.75e+01 bond pdb=" N GLY A 213 " pdb=" H GLY A 213 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.67e+01 bond pdb=" N ALA A 217 " pdb=" H ALA A 217 " ideal model delta sigma weight residual 0.860 1.035 -0.175 2.00e-02 2.50e+03 7.66e+01 ... (remaining 30223 not shown) Histogram of bond angle deviations from ideal: 75.15 - 86.92: 4 86.92 - 98.69: 1 98.69 - 110.45: 30406 110.45 - 122.22: 19767 122.22 - 133.99: 4386 Bond angle restraints: 54564 Sorted by residual: angle pdb=" N PRO A 216 " pdb=" CA PRO A 216 " pdb=" CB PRO A 216 " ideal model delta sigma weight residual 102.60 96.86 5.74 1.10e+00 8.26e-01 2.73e+01 angle pdb=" C ASP A 212 " pdb=" CA ASP A 212 " pdb=" CB ASP A 212 " ideal model delta sigma weight residual 109.66 118.57 -8.91 1.94e+00 2.66e-01 2.11e+01 angle pdb=" N PHE A 136 " pdb=" CA PHE A 136 " pdb=" CB PHE A 136 " ideal model delta sigma weight residual 114.17 109.83 4.34 1.14e+00 7.69e-01 1.45e+01 angle pdb=" C PRO A 216 " pdb=" N ALA A 217 " pdb=" CA ALA A 217 " ideal model delta sigma weight residual 120.60 126.58 -5.98 1.60e+00 3.91e-01 1.40e+01 angle pdb=" C SER B 44 " pdb=" N SER B 45 " pdb=" CA SER B 45 " ideal model delta sigma weight residual 121.70 127.65 -5.95 1.80e+00 3.09e-01 1.09e+01 ... (remaining 54559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.96: 13619 34.96 - 69.92: 286 69.92 - 104.88: 35 104.88 - 139.83: 6 139.83 - 174.79: 3 Dihedral angle restraints: 13949 sinusoidal: 7495 harmonic: 6454 Sorted by residual: dihedral pdb=" C5' FMN B 501 " pdb=" O5' FMN B 501 " pdb=" P FMN B 501 " pdb=" O1P FMN B 501 " ideal model delta sinusoidal sigma weight residual 75.26 -109.95 -174.79 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" C10 FMN C1000 " pdb=" C1' FMN C1000 " pdb=" N10 FMN C1000 " pdb=" C2' FMN C1000 " ideal model delta sinusoidal sigma weight residual -102.41 70.90 -173.31 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C10 FMN B 501 " pdb=" C1' FMN B 501 " pdb=" N10 FMN B 501 " pdb=" C2' FMN B 501 " ideal model delta sinusoidal sigma weight residual 257.59 90.40 167.19 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 13946 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1927 0.047 - 0.094: 300 0.094 - 0.141: 112 0.141 - 0.188: 1 0.188 - 0.235: 9 Chirality restraints: 2349 Sorted by residual: chirality pdb=" C4' LMT B 504 " pdb=" C3' LMT B 504 " pdb=" C5' LMT B 504 " pdb=" O1B LMT B 504 " both_signs ideal model delta sigma weight residual False -2.55 -2.79 0.24 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" C4' LMT B 503 " pdb=" C3' LMT B 503 " pdb=" C5' LMT B 503 " pdb=" O1B LMT B 503 " both_signs ideal model delta sigma weight residual False -2.55 -2.78 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" C5' LMT D 302 " pdb=" C4' LMT D 302 " pdb=" C6' LMT D 302 " pdb=" O5' LMT D 302 " both_signs ideal model delta sigma weight residual False -2.51 -2.30 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2346 not shown) Planarity restraints: 4416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 UQ1 B 506 " 0.016 2.00e-02 2.50e+03 4.40e-02 5.81e+01 pdb=" C2 UQ1 B 506 " 0.019 2.00e-02 2.50e+03 pdb=" C3 UQ1 B 506 " -0.031 2.00e-02 2.50e+03 pdb=" C4 UQ1 B 506 " 0.011 2.00e-02 2.50e+03 pdb=" C5 UQ1 B 506 " 0.013 2.00e-02 2.50e+03 pdb=" C6 UQ1 B 506 " -0.022 2.00e-02 2.50e+03 pdb=" C7 UQ1 B 506 " -0.084 2.00e-02 2.50e+03 pdb=" CM5 UQ1 B 506 " 0.048 2.00e-02 2.50e+03 pdb=" O1 UQ1 B 506 " 0.035 2.00e-02 2.50e+03 pdb=" O2 UQ1 B 506 " 0.048 2.00e-02 2.50e+03 pdb=" O3 UQ1 B 506 " -0.083 2.00e-02 2.50e+03 pdb=" O4 UQ1 B 506 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 211 " -0.017 2.00e-02 2.50e+03 3.34e-02 1.12e+01 pdb=" C PHE A 211 " 0.058 2.00e-02 2.50e+03 pdb=" O PHE A 211 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP A 212 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 212 " -0.014 2.00e-02 2.50e+03 2.94e-02 8.65e+00 pdb=" C ASP A 212 " 0.051 2.00e-02 2.50e+03 pdb=" O ASP A 212 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY A 213 " -0.017 2.00e-02 2.50e+03 ... (remaining 4413 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1371 2.18 - 2.78: 60657 2.78 - 3.39: 88625 3.39 - 3.99: 117721 3.99 - 4.60: 180497 Nonbonded interactions: 448871 Sorted by model distance: nonbonded pdb=" O TRP C 238 " pdb=" H PHE C 244 " model vdw 1.572 1.850 nonbonded pdb=" O PRO E 114 " pdb=" HG1 THR E 117 " model vdw 1.593 1.850 nonbonded pdb=" O ASP C 77 " pdb=" H GLY C 81 " model vdw 1.615 1.850 nonbonded pdb=" OE1 GLU F 371 " pdb=" H GLU F 371 " model vdw 1.617 1.850 nonbonded pdb="HE22 GLN A 242 " pdb=" O VAL A 261 " model vdw 1.628 1.850 ... (remaining 448866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 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: 0.510 Extract box with map and model: 8.890 Check model and map are aligned: 0.440 Set scattering table: 0.270 Process input model: 109.010 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 135.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.004 0.076 15452 Z= 0.237 Angle : 0.562 9.563 20923 Z= 0.266 Chirality : 0.041 0.235 2349 Planarity : 0.003 0.050 2599 Dihedral : 16.543 174.794 5815 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.32 % Allowed : 10.78 % Favored : 88.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.20), residues: 1896 helix: 1.92 (0.18), residues: 871 sheet: 0.39 (0.40), residues: 181 loop : 0.51 (0.22), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 226 HIS 0.003 0.001 HIS B 46 PHE 0.011 0.001 PHE B 213 TYR 0.007 0.001 TYR F 217 ARG 0.004 0.000 ARG B 43 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 285 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 280 time to evaluate : 2.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 285 average time/residue: 2.6142 time to fit residues: 827.0617 Evaluate side-chains 188 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 184 time to evaluate : 2.387 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 2.9143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 158 optimal weight: 9.9990 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 147 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 109 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 170 GLN A 249 GLN B 84 ASN C 51 GLN D 64 ASN E 92 GLN F 112 GLN ** F 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 330 ASN F 336 HIS ** F 356 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15452 Z= 0.259 Angle : 0.557 7.145 20923 Z= 0.291 Chirality : 0.043 0.288 2349 Planarity : 0.004 0.065 2599 Dihedral : 13.305 176.596 2461 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.99 % Allowed : 15.47 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.19), residues: 1896 helix: 1.29 (0.18), residues: 867 sheet: 0.41 (0.40), residues: 165 loop : 0.28 (0.21), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 70 HIS 0.005 0.001 HIS A 223 PHE 0.019 0.001 PHE D 50 TYR 0.017 0.002 TYR F 307 ARG 0.004 0.001 ARG F 303 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 215 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 184 time to evaluate : 2.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 18 residues processed: 206 average time/residue: 2.3567 time to fit residues: 547.2018 Evaluate side-chains 183 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 165 time to evaluate : 2.352 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 12 residues processed: 6 average time/residue: 0.6740 time to fit residues: 8.7316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 94 optimal weight: 0.5980 chunk 52 optimal weight: 4.9990 chunk 142 optimal weight: 6.9990 chunk 116 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 171 optimal weight: 7.9990 chunk 184 optimal weight: 8.9990 chunk 152 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 137 optimal weight: 6.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 ASN D 64 ASN ** F 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 356 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7107 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 15452 Z= 0.364 Angle : 0.608 8.018 20923 Z= 0.315 Chirality : 0.045 0.407 2349 Planarity : 0.005 0.058 2599 Dihedral : 12.845 172.088 2461 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.63 % Allowed : 15.98 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.19), residues: 1896 helix: 0.88 (0.18), residues: 866 sheet: -0.24 (0.38), residues: 178 loop : -0.09 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 70 HIS 0.006 0.001 HIS A 223 PHE 0.022 0.002 PHE D 50 TYR 0.014 0.002 TYR D 141 ARG 0.007 0.001 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 209 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 168 time to evaluate : 2.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 24 residues processed: 195 average time/residue: 2.4205 time to fit residues: 531.1441 Evaluate side-chains 182 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 158 time to evaluate : 2.435 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 17 residues processed: 7 average time/residue: 0.8094 time to fit residues: 10.6606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 168 optimal weight: 6.9990 chunk 128 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 114 optimal weight: 5.9990 chunk 171 optimal weight: 3.9990 chunk 181 optimal weight: 5.9990 chunk 89 optimal weight: 1.9990 chunk 162 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15452 Z= 0.281 Angle : 0.562 8.622 20923 Z= 0.290 Chirality : 0.043 0.426 2349 Planarity : 0.004 0.055 2599 Dihedral : 12.261 171.808 2461 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 2.25 % Allowed : 17.07 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.19), residues: 1896 helix: 0.85 (0.18), residues: 869 sheet: -0.06 (0.38), residues: 164 loop : -0.14 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 70 HIS 0.004 0.001 HIS B 330 PHE 0.020 0.002 PHE B 213 TYR 0.014 0.002 TYR D 141 ARG 0.004 0.001 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 200 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 165 time to evaluate : 2.555 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 22 residues processed: 190 average time/residue: 2.2555 time to fit residues: 483.8162 Evaluate side-chains 177 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 155 time to evaluate : 1.775 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 18 residues processed: 4 average time/residue: 0.6591 time to fit residues: 5.7850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 151 optimal weight: 5.9990 chunk 103 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 135 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 92 optimal weight: 6.9990 chunk 163 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 203 GLN ** F 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 15452 Z= 0.239 Angle : 0.540 8.799 20923 Z= 0.277 Chirality : 0.042 0.441 2349 Planarity : 0.004 0.054 2599 Dihedral : 11.897 171.379 2461 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.99 % Allowed : 17.91 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.19), residues: 1896 helix: 0.91 (0.18), residues: 871 sheet: -0.08 (0.38), residues: 162 loop : -0.13 (0.20), residues: 863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 103 HIS 0.003 0.001 HIS B 330 PHE 0.019 0.001 PHE F 267 TYR 0.013 0.001 TYR D 141 ARG 0.003 0.000 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 194 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 163 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 25 residues processed: 184 average time/residue: 2.0811 time to fit residues: 435.5056 Evaluate side-chains 179 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 2.598 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 19 residues processed: 6 average time/residue: 1.6250 time to fit residues: 14.3398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 61 optimal weight: 0.5980 chunk 163 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 106 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 chunk 150 optimal weight: 6.9990 chunk 84 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 95 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 15452 Z= 0.250 Angle : 0.541 8.586 20923 Z= 0.277 Chirality : 0.042 0.436 2349 Planarity : 0.004 0.054 2599 Dihedral : 11.866 171.300 2461 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.31 % Allowed : 17.65 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.19), residues: 1896 helix: 0.92 (0.18), residues: 872 sheet: -0.18 (0.38), residues: 162 loop : -0.14 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 103 HIS 0.004 0.001 HIS B 330 PHE 0.023 0.001 PHE D 50 TYR 0.012 0.001 TYR D 141 ARG 0.004 0.001 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 157 time to evaluate : 2.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 25 residues processed: 186 average time/residue: 1.8329 time to fit residues: 386.2386 Evaluate side-chains 179 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 154 time to evaluate : 1.451 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 0.8971 time to fit residues: 6.1616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 175 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 103 optimal weight: 4.9990 chunk 132 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 153 optimal weight: 9.9990 chunk 101 optimal weight: 2.9990 chunk 181 optimal weight: 10.0000 chunk 113 optimal weight: 5.9990 chunk 110 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 244 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7108 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15452 Z= 0.287 Angle : 0.562 8.394 20923 Z= 0.289 Chirality : 0.043 0.422 2349 Planarity : 0.004 0.054 2599 Dihedral : 11.985 171.459 2461 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.37 % Allowed : 17.39 % Favored : 80.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.35 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.19), residues: 1896 helix: 0.88 (0.18), residues: 869 sheet: -0.33 (0.38), residues: 169 loop : -0.20 (0.20), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 70 HIS 0.005 0.001 HIS A 313 PHE 0.021 0.002 PHE F 267 TYR 0.015 0.002 TYR F 217 ARG 0.004 0.001 ARG D 199 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3792 Ramachandran restraints generated. 1896 Oldfield, 0 Emsley, 1896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 236 is missing expected H atoms. Skipping. Residue THR 225 is missing expected H atoms. Skipping. Evaluate side-chains 193 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 156 time to evaluate : 3.055 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 25 residues processed: 184 average time/residue: 2.2621 time to fit residues: 472.8484 Evaluate side-chains 175 residues out of total 1558 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 150 time to evaluate : 2.323 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 4 average time/residue: 1.6322 time to fit residues: 10.4960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 188 random chunks: chunk 112 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 108 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 123 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 142 optimal weight: 5.9990 chunk 164 optimal weight: 0.1980 overall best weight: 2.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: