Starting phenix.real_space_refine on Fri Feb 16 05:40:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/02_2024/8g4c_29716_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/02_2024/8g4c_29716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/02_2024/8g4c_29716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/02_2024/8g4c_29716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/02_2024/8g4c_29716_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8g4c_29716/02_2024/8g4c_29716_updated.pdb" } resolution = 3.1 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= 0.029 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: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 64 5.16 5 C 9388 2.51 5 N 2401 2.21 5 O 2643 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 21": "OE1" <-> "OE2" Residue "B GLU 76": "OE1" <-> "OE2" Residue "B TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 34": "OE1" <-> "OE2" Residue "C GLU 81": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14503 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 5036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 639, 5036 Classifications: {'peptide': 639} Link IDs: {'PTRANS': 10, 'TRANS': 628} Chain breaks: 1 Chain: "B" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "C" Number of atoms: 1940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1940 Classifications: {'peptide': 248} Link IDs: {'PTRANS': 5, 'TRANS': 242} Chain: "D" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "E" Number of atoms: 2738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2738 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 324} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'6OU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'AGS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.80, per 1000 atoms: 0.54 Number of scatterers: 14503 At special positions: 0 Unit cell: (108.128, 123.824, 192.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 7 15.00 O 2643 8.00 N 2401 7.00 C 9388 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 5.44 Conformation dependent library (CDL) restraints added in 3.0 seconds 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3390 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 71 helices and 10 sheets defined 56.0% alpha, 8.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.14 Creating SS restraints... Processing helix chain 'A' and resid 3 through 17 removed outlier: 5.433A pdb=" N ARG A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N ASN A 17 " --> pdb=" O LYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 38 removed outlier: 4.129A pdb=" N LEU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 46 removed outlier: 3.629A pdb=" N ASN A 45 " --> pdb=" O PRO A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 56 through 81 removed outlier: 3.738A pdb=" N ALA A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N PHE A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N THR A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N PHE A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 93 Processing helix chain 'A' and resid 97 through 138 removed outlier: 3.938A pdb=" N ARG A 102 " --> pdb=" O HIS A 98 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU A 107 " --> pdb=" O ILE A 103 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N ASN A 108 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL A 109 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N MET A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ALA A 121 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 127 " --> pdb=" O GLY A 123 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N LYS A 128 " --> pdb=" O PHE A 124 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N LEU A 129 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 130 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LEU A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 176 removed outlier: 3.788A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N LEU A 166 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 173 " --> pdb=" O ILE A 169 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N PHE A 174 " --> pdb=" O MET A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 183 removed outlier: 3.623A pdb=" N LEU A 183 " --> pdb=" O ILE A 180 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 180 through 183' Processing helix chain 'A' and resid 199 through 224 removed outlier: 4.053A pdb=" N ALA A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ILE A 209 " --> pdb=" O GLY A 205 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 266 removed outlier: 3.663A pdb=" N PHE A 234 " --> pdb=" O ILE A 230 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL A 235 " --> pdb=" O ASN A 231 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL A 256 " --> pdb=" O TYR A 252 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N THR A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE A 259 " --> pdb=" O SER A 255 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER A 266 " --> pdb=" O ILE A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 288 removed outlier: 3.798A pdb=" N SER A 280 " --> pdb=" O VAL A 276 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N SER A 281 " --> pdb=" O LEU A 277 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N PHE A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET A 286 " --> pdb=" O ILE A 282 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N LYS A 287 " --> pdb=" O MET A 283 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 315 removed outlier: 3.853A pdb=" N ILE A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 324 Processing helix chain 'A' and resid 334 through 347 removed outlier: 4.122A pdb=" N GLU A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N SER A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 415 Processing helix chain 'A' and resid 448 through 451 No H-bonds generated for 'chain 'A' and resid 448 through 451' Processing helix chain 'A' and resid 462 through 471 Processing helix chain 'A' and resid 494 through 504 Processing helix chain 'A' and resid 513 through 553 removed outlier: 3.887A pdb=" N ALA A 518 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ALA A 519 " --> pdb=" O ASP A 515 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N GLN A 520 " --> pdb=" O THR A 516 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N LYS A 521 " --> pdb=" O SER A 517 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N MET A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY A 543 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLY A 552 " --> pdb=" O PHE A 548 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU A 553 " --> pdb=" O LYS A 549 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 562 Processing helix chain 'A' and resid 571 through 586 removed outlier: 3.810A pdb=" N LYS A 576 " --> pdb=" O GLY A 572 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N GLY A 577 " --> pdb=" O ASP A 573 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ILE A 578 " --> pdb=" O LEU A 574 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE A 580 " --> pdb=" O LYS A 576 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N MET A 583 " --> pdb=" O ARG A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 588 through 602 Processing helix chain 'A' and resid 604 through 607 No H-bonds generated for 'chain 'A' and resid 604 through 607' Processing helix chain 'A' and resid 614 through 643 removed outlier: 3.831A pdb=" N MET A 618 " --> pdb=" O ALA A 614 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL A 621 " --> pdb=" O ILE A 617 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N LEU A 622 " --> pdb=" O MET A 618 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 623 " --> pdb=" O VAL A 619 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 624 " --> pdb=" O MET A 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 16 through 18 No H-bonds generated for 'chain 'B' and resid 16 through 18' Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 77 through 86 removed outlier: 3.644A pdb=" N GLN B 85 " --> pdb=" O GLU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 109 through 112 removed outlier: 3.626A pdb=" N ILE B 112 " --> pdb=" O PRO B 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 109 through 112' Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.174A pdb=" N LYS B 123 " --> pdb=" O GLU B 119 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 125 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N VAL B 127 " --> pdb=" O LYS B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 141 through 143 No H-bonds generated for 'chain 'B' and resid 141 through 143' Processing helix chain 'B' and resid 146 through 158 removed outlier: 3.516A pdb=" N GLN B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 192 Processing helix chain 'B' and resid 204 through 209 removed outlier: 4.290A pdb=" N TYR B 209 " --> pdb=" O VAL B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 247 removed outlier: 3.767A pdb=" N VAL B 245 " --> pdb=" O LYS B 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LEU B 246 " --> pdb=" O THR B 242 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 247 " --> pdb=" O GLN B 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 53 Processing helix chain 'C' and resid 76 through 86 Processing helix chain 'C' and resid 102 through 111 removed outlier: 3.568A pdb=" N LEU C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Proline residue: C 109 - end of helix Processing helix chain 'C' and resid 117 through 131 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 146 through 158 removed outlier: 3.740A pdb=" N ALA C 157 " --> pdb=" O SER C 153 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N PHE C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 192 removed outlier: 3.543A pdb=" N GLN C 191 " --> pdb=" O SER C 187 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LYS C 192 " --> pdb=" O GLN C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 209 No H-bonds generated for 'chain 'C' and resid 207 through 209' Processing helix chain 'C' and resid 234 through 247 removed outlier: 3.540A pdb=" N VAL C 245 " --> pdb=" O LYS C 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 8 Processing helix chain 'D' and resid 10 through 29 Processing helix chain 'D' and resid 37 through 60 Processing helix chain 'D' and resid 63 through 71 Processing helix chain 'D' and resid 85 through 137 removed outlier: 3.638A pdb=" N VAL D 90 " --> pdb=" O PHE D 86 " (cutoff:3.500A) Proline residue: D 129 - end of helix Processing helix chain 'D' and resid 144 through 170 removed outlier: 4.442A pdb=" N SER D 170 " --> pdb=" O GLN D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 193 Processing helix chain 'D' and resid 195 through 201 Processing helix chain 'D' and resid 218 through 234 Processing helix chain 'D' and resid 265 through 272 Proline residue: D 269 - end of helix removed outlier: 4.865A pdb=" N PHE D 272 " --> pdb=" O VAL D 268 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 265 through 272' Processing helix chain 'D' and resid 282 through 284 No H-bonds generated for 'chain 'D' and resid 282 through 284' Processing helix chain 'D' and resid 291 through 301 removed outlier: 3.546A pdb=" N ALA D 300 " --> pdb=" O LYS D 296 " (cutoff:3.500A) Proline residue: D 301 - end of helix Processing helix chain 'D' and resid 325 through 333 removed outlier: 3.603A pdb=" N GLU D 329 " --> pdb=" O ASN D 326 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS D 330 " --> pdb=" O GLN D 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 8 Processing helix chain 'E' and resid 11 through 29 removed outlier: 3.781A pdb=" N GLN E 19 " --> pdb=" O ALA E 15 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLN E 20 " --> pdb=" O PHE E 16 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N PHE E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 60 removed outlier: 3.766A pdb=" N TYR E 40 " --> pdb=" O GLY E 36 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N MET E 41 " --> pdb=" O ASN E 37 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N PHE E 48 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG E 58 " --> pdb=" O TRP E 54 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LYS E 59 " --> pdb=" O PHE E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 Processing helix chain 'E' and resid 85 through 137 removed outlier: 3.754A pdb=" N VAL E 90 " --> pdb=" O PHE E 86 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU E 91 " --> pdb=" O GLU E 87 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER E 93 " --> pdb=" O MET E 89 " (cutoff:3.500A) Proline residue: E 129 - end of helix Processing helix chain 'E' and resid 144 through 168 Processing helix chain 'E' and resid 183 through 193 Processing helix chain 'E' and resid 195 through 201 Processing helix chain 'E' and resid 218 through 235 Processing helix chain 'E' and resid 265 through 267 No H-bonds generated for 'chain 'E' and resid 265 through 267' Processing helix chain 'E' and resid 282 through 286 Processing helix chain 'E' and resid 291 through 301 Proline residue: E 301 - end of helix Processing helix chain 'E' and resid 325 through 327 No H-bonds generated for 'chain 'E' and resid 325 through 327' Processing sheet with id= A, first strand: chain 'B' and resid 63 through 66 removed outlier: 7.024A pdb=" N ILE B 30 " --> pdb=" O ILE B 3 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N GLU B 5 " --> pdb=" O ILE B 28 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE B 28 " --> pdb=" O GLU B 5 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 221 through 226 removed outlier: 6.839A pdb=" N PHE B 215 " --> pdb=" O TYR B 222 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN B 224 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL B 213 " --> pdb=" O GLN B 224 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG B 212 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ILE B 197 " --> pdb=" O VAL B 36 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N ILE B 38 " --> pdb=" O ILE B 197 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N MET B 199 " --> pdb=" O ILE B 38 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 9 through 11 removed outlier: 3.661A pdb=" N ILE B 26 " --> pdb=" O ILE B 9 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N LYS B 11 " --> pdb=" O LYS B 24 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N LYS B 24 " --> pdb=" O LYS B 11 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 63 through 66 removed outlier: 3.584A pdb=" N THR C 63 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N ILE C 30 " --> pdb=" O ILE C 3 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLU C 5 " --> pdb=" O ILE C 28 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE C 28 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'C' and resid 12 through 15 removed outlier: 3.512A pdb=" N ASN C 18 " --> pdb=" O ASN C 15 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 224 through 226 Processing sheet with id= G, first strand: chain 'C' and resid 9 through 11 removed outlier: 3.677A pdb=" N ILE C 26 " --> pdb=" O ILE C 9 " (cutoff:3.500A) removed outlier: 8.243A pdb=" N LYS C 11 " --> pdb=" O LYS C 24 " (cutoff:3.500A) removed outlier: 5.831A pdb=" N LYS C 24 " --> pdb=" O LYS C 11 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 179 through 182 removed outlier: 3.860A pdb=" N GLU D 179 " --> pdb=" O SER D 216 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N SER D 216 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 205 through 209 removed outlier: 7.600A pdb=" N ILE D 241 " --> pdb=" O ASP D 206 " (cutoff:3.500A) removed outlier: 8.527A pdb=" N GLN D 208 " --> pdb=" O ILE D 241 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N ILE D 243 " --> pdb=" O GLN D 208 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LYS D 248 " --> pdb=" O GLN D 251 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N HIS D 305 " --> pdb=" O THR D 321 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'E' and resid 205 through 209 removed outlier: 6.896A pdb=" N ILE E 241 " --> pdb=" O ASP E 206 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N GLN E 208 " --> pdb=" O ILE E 241 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE E 243 " --> pdb=" O GLN E 208 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N HIS E 305 " --> pdb=" O THR E 321 " (cutoff:3.500A) 706 hydrogen bonds defined for protein. 2073 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.24 Time building geometry restraints manager: 5.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 4574 1.34 - 1.50: 3705 1.50 - 1.65: 6383 1.65 - 1.80: 62 1.80 - 1.95: 56 Bond restraints: 14780 Sorted by residual: bond pdb=" C16 6OU A 701 " pdb=" O18 6OU A 701 " ideal model delta sigma weight residual 1.327 1.463 -0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C31 6OU A 701 " pdb=" O30 6OU A 701 " ideal model delta sigma weight residual 1.331 1.423 -0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" C14 6OU A 701 " pdb=" C15 6OU A 701 " ideal model delta sigma weight residual 1.521 1.607 -0.086 2.00e-02 2.50e+03 1.83e+01 bond pdb=" C15 6OU A 701 " pdb=" C16 6OU A 701 " ideal model delta sigma weight residual 1.501 1.583 -0.082 2.00e-02 2.50e+03 1.67e+01 bond pdb=" C41 6OU A 701 " pdb=" C42 6OU A 701 " ideal model delta sigma weight residual 1.497 1.568 -0.071 2.00e-02 2.50e+03 1.27e+01 ... (remaining 14775 not shown) Histogram of bond angle deviations from ideal: 98.92 - 109.76: 1387 109.76 - 120.60: 13444 120.60 - 131.45: 5060 131.45 - 142.29: 19 142.29 - 153.13: 1 Bond angle restraints: 19911 Sorted by residual: angle pdb=" C40 6OU A 701 " pdb=" C41 6OU A 701 " pdb=" C42 6OU A 701 " ideal model delta sigma weight residual 127.56 153.13 -25.57 3.00e+00 1.11e-01 7.27e+01 angle pdb=" CA PRO E 129 " pdb=" N PRO E 129 " pdb=" CD PRO E 129 " ideal model delta sigma weight residual 112.00 102.89 9.11 1.40e+00 5.10e-01 4.24e+01 angle pdb=" O22 6OU A 701 " pdb=" P23 6OU A 701 " pdb=" O26 6OU A 701 " ideal model delta sigma weight residual 93.95 109.56 -15.61 3.00e+00 1.11e-01 2.71e+01 angle pdb=" C39 6OU A 701 " pdb=" C40 6OU A 701 " pdb=" C41 6OU A 701 " ideal model delta sigma weight residual 127.60 112.85 14.75 3.00e+00 1.11e-01 2.42e+01 angle pdb=" N ASP A 556 " pdb=" CA ASP A 556 " pdb=" C ASP A 556 " ideal model delta sigma weight residual 112.89 106.81 6.08 1.24e+00 6.50e-01 2.41e+01 ... (remaining 19906 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.91: 8609 32.91 - 65.82: 267 65.82 - 98.74: 30 98.74 - 131.65: 0 131.65 - 164.56: 6 Dihedral angle restraints: 8912 sinusoidal: 3672 harmonic: 5240 Sorted by residual: dihedral pdb=" C19 6OU A 701 " pdb=" C20 6OU A 701 " pdb=" O30 6OU A 701 " pdb=" C31 6OU A 701 " ideal model delta sinusoidal sigma weight residual 212.33 47.77 164.56 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C19 6OU A 701 " pdb=" C20 6OU A 701 " pdb=" C21 6OU A 701 " pdb=" O22 6OU A 701 " ideal model delta sinusoidal sigma weight residual -59.00 103.83 -162.83 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" C21 6OU A 701 " pdb=" C20 6OU A 701 " pdb=" O30 6OU A 701 " pdb=" C31 6OU A 701 " ideal model delta sinusoidal sigma weight residual 85.49 -75.42 160.91 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 8909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1559 0.035 - 0.070: 496 0.070 - 0.105: 151 0.105 - 0.140: 57 0.140 - 0.176: 5 Chirality restraints: 2268 Sorted by residual: chirality pdb=" CA PRO E 129 " pdb=" N PRO E 129 " pdb=" C PRO E 129 " pdb=" CB PRO E 129 " both_signs ideal model delta sigma weight residual False 2.72 2.54 0.18 2.00e-01 2.50e+01 7.70e-01 chirality pdb=" CA VAL C 245 " pdb=" N VAL C 245 " pdb=" C VAL C 245 " pdb=" CB VAL C 245 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.16 2.00e-01 2.50e+01 6.80e-01 chirality pdb=" CG LEU E 119 " pdb=" CB LEU E 119 " pdb=" CD1 LEU E 119 " pdb=" CD2 LEU E 119 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.45e-01 ... (remaining 2265 not shown) Planarity restraints: 2479 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR E 128 " 0.062 5.00e-02 4.00e+02 8.82e-02 1.25e+01 pdb=" N PRO E 129 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO E 129 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 129 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET C 240 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C MET C 240 " -0.035 2.00e-02 2.50e+03 pdb=" O MET C 240 " 0.013 2.00e-02 2.50e+03 pdb=" N LYS C 241 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 84 " 0.029 5.00e-02 4.00e+02 4.36e-02 3.04e+00 pdb=" N PRO D 85 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO D 85 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 85 " 0.024 5.00e-02 4.00e+02 ... (remaining 2476 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2444 2.77 - 3.30: 13520 3.30 - 3.83: 22891 3.83 - 4.37: 25480 4.37 - 4.90: 45818 Nonbonded interactions: 110153 Sorted by model distance: nonbonded pdb=" O SER A 125 " pdb=" OH TYR E 40 " model vdw 2.236 2.440 nonbonded pdb=" OG SER B 145 " pdb=" OE1 GLN B 148 " model vdw 2.245 2.440 nonbonded pdb=" OG SER A 406 " pdb=" O GLU A 443 " model vdw 2.282 2.440 nonbonded pdb=" O SER A 316 " pdb=" OG SER A 316 " model vdw 2.303 2.440 nonbonded pdb=" OD1 ASP A 410 " pdb=" N LEU A 411 " model vdw 2.306 2.520 ... (remaining 110148 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' } 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: 2.270 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: 0.010 Extract box with map and model: 10.280 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 39.870 Find NCS groups from input model: 0.600 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 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 0.136 14780 Z= 0.248 Angle : 0.593 25.574 19911 Z= 0.303 Chirality : 0.041 0.176 2268 Planarity : 0.003 0.088 2479 Dihedral : 16.586 164.560 5522 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 0.25 % Allowed : 0.83 % Favored : 98.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.21), residues: 1791 helix: 1.53 (0.17), residues: 1034 sheet: -0.16 (0.40), residues: 190 loop : -1.22 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 605 HIS 0.003 0.001 HIS A 596 PHE 0.013 0.001 PHE C 235 TYR 0.023 0.001 TYR A 623 ARG 0.002 0.000 ARG E 168 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 137 time to evaluate : 1.594 Fit side-chains revert: symmetry clash REVERT: A 37 THR cc_start: 0.8183 (t) cc_final: 0.7967 (t) REVERT: A 319 LYS cc_start: 0.7671 (ttpt) cc_final: 0.7467 (ttmt) REVERT: D 58 ARG cc_start: 0.6598 (tmm-80) cc_final: 0.6352 (ttt180) REVERT: D 100 HIS cc_start: 0.5351 (t-90) cc_final: 0.4991 (t-170) outliers start: 4 outliers final: 1 residues processed: 140 average time/residue: 0.2807 time to fit residues: 57.4761 Evaluate side-chains 119 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 118 time to evaluate : 1.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 243 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 149 optimal weight: 0.9980 chunk 134 optimal weight: 8.9990 chunk 74 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 138 optimal weight: 9.9990 chunk 53 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 103 optimal weight: 2.9990 chunk 160 optimal weight: 0.0970 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.0546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14780 Z= 0.194 Angle : 0.474 7.798 19911 Z= 0.252 Chirality : 0.040 0.165 2268 Planarity : 0.003 0.042 2479 Dihedral : 11.525 158.475 1999 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.89 % Allowed : 6.37 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1791 helix: 1.59 (0.17), residues: 1031 sheet: -0.27 (0.39), residues: 191 loop : -1.31 (0.25), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.013 0.001 PHE C 235 TYR 0.020 0.001 TYR A 623 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.554 Fit side-chains revert: symmetry clash REVERT: A 319 LYS cc_start: 0.7727 (ttpt) cc_final: 0.7514 (ttmt) REVERT: D 89 MET cc_start: 0.6411 (tpp) cc_final: 0.5424 (mtt) REVERT: D 100 HIS cc_start: 0.5383 (t-90) cc_final: 0.5059 (t70) outliers start: 14 outliers final: 8 residues processed: 127 average time/residue: 0.2774 time to fit residues: 53.6613 Evaluate side-chains 125 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 1.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 560 SER Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain D residue 94 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 133 optimal weight: 20.0000 chunk 109 optimal weight: 2.9990 chunk 44 optimal weight: 30.0000 chunk 161 optimal weight: 8.9990 chunk 173 optimal weight: 9.9990 chunk 143 optimal weight: 10.0000 chunk 159 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 129 optimal weight: 0.0050 overall best weight: 1.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 ASN E 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.0999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14780 Z= 0.281 Angle : 0.529 8.255 19911 Z= 0.279 Chirality : 0.042 0.200 2268 Planarity : 0.003 0.041 2479 Dihedral : 11.131 159.218 1996 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.40 % Allowed : 9.48 % Favored : 89.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.21), residues: 1791 helix: 1.38 (0.17), residues: 1033 sheet: -0.34 (0.39), residues: 188 loop : -1.39 (0.25), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 605 HIS 0.005 0.001 HIS B 202 PHE 0.015 0.002 PHE C 235 TYR 0.023 0.002 TYR A 623 ARG 0.003 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.741 Fit side-chains REVERT: A 70 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8683 (mt) REVERT: A 376 MET cc_start: -0.0801 (pmm) cc_final: -0.1535 (mmm) REVERT: A 607 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.8017 (pp) REVERT: B 221 MET cc_start: 0.7561 (OUTLIER) cc_final: 0.6357 (mmt) REVERT: C 246 LEU cc_start: 0.7432 (OUTLIER) cc_final: 0.7217 (tp) REVERT: D 100 HIS cc_start: 0.5382 (t-90) cc_final: 0.5040 (t70) outliers start: 22 outliers final: 14 residues processed: 125 average time/residue: 0.2591 time to fit residues: 49.1108 Evaluate side-chains 128 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 1.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 76 optimal weight: 0.0980 chunk 108 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 171 optimal weight: 20.0000 chunk 84 optimal weight: 1.9990 chunk 153 optimal weight: 0.9990 chunk 46 optimal weight: 6.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14780 Z= 0.160 Angle : 0.452 7.611 19911 Z= 0.241 Chirality : 0.039 0.156 2268 Planarity : 0.003 0.039 2479 Dihedral : 10.875 159.638 1996 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.53 % Allowed : 11.52 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1791 helix: 1.54 (0.17), residues: 1028 sheet: -0.30 (0.39), residues: 189 loop : -1.40 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.013 0.001 PHE D 52 TYR 0.016 0.001 TYR A 623 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 116 time to evaluate : 1.691 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8556 (mp) REVERT: A 376 MET cc_start: -0.0801 (pmm) cc_final: -0.1560 (mmm) REVERT: B 221 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.6352 (mmt) REVERT: D 100 HIS cc_start: 0.5291 (t-90) cc_final: 0.4942 (t70) outliers start: 24 outliers final: 13 residues processed: 133 average time/residue: 0.2557 time to fit residues: 51.6760 Evaluate side-chains 127 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 112 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 142 optimal weight: 20.0000 chunk 97 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 127 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 145 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 0 optimal weight: 5.9990 chunk 87 optimal weight: 1.9990 chunk 153 optimal weight: 5.9990 chunk 43 optimal weight: 0.0980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7494 moved from start: 0.1031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 14780 Z= 0.176 Angle : 0.457 7.633 19911 Z= 0.242 Chirality : 0.040 0.165 2268 Planarity : 0.003 0.038 2479 Dihedral : 10.701 160.340 1996 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.59 % Allowed : 12.22 % Favored : 86.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.21), residues: 1791 helix: 1.58 (0.17), residues: 1027 sheet: -0.30 (0.38), residues: 189 loop : -1.40 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.014 0.001 TYR A 623 ARG 0.002 0.000 ARG E 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 113 time to evaluate : 1.576 Fit side-chains revert: symmetry clash REVERT: A 70 ILE cc_start: 0.9017 (OUTLIER) cc_final: 0.8547 (mp) REVERT: A 376 MET cc_start: -0.0877 (pmm) cc_final: -0.1504 (mmm) REVERT: A 607 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.7966 (pp) REVERT: B 221 MET cc_start: 0.7528 (OUTLIER) cc_final: 0.6404 (mmt) REVERT: D 100 HIS cc_start: 0.5263 (t-90) cc_final: 0.4910 (t70) outliers start: 25 outliers final: 21 residues processed: 129 average time/residue: 0.2549 time to fit residues: 50.4577 Evaluate side-chains 136 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 112 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 57 optimal weight: 0.7980 chunk 154 optimal weight: 3.9990 chunk 33 optimal weight: 9.9990 chunk 100 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 171 optimal weight: 20.0000 chunk 142 optimal weight: 30.0000 chunk 79 optimal weight: 0.8980 chunk 14 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 89 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 142 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14780 Z= 0.202 Angle : 0.470 7.726 19911 Z= 0.248 Chirality : 0.040 0.171 2268 Planarity : 0.003 0.037 2479 Dihedral : 10.627 159.838 1996 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 1.72 % Allowed : 13.18 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.21), residues: 1791 helix: 1.56 (0.17), residues: 1027 sheet: -0.33 (0.38), residues: 189 loop : -1.41 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 605 HIS 0.004 0.001 HIS B 202 PHE 0.012 0.001 PHE D 52 TYR 0.014 0.001 TYR A 164 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 109 time to evaluate : 1.649 Fit side-chains REVERT: A 70 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8546 (mp) REVERT: A 376 MET cc_start: -0.0872 (pmm) cc_final: -0.1395 (mmm) REVERT: A 607 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8066 (pp) REVERT: C 69 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.8202 (m-40) REVERT: D 100 HIS cc_start: 0.5322 (t-90) cc_final: 0.4949 (t70) outliers start: 27 outliers final: 22 residues processed: 128 average time/residue: 0.2536 time to fit residues: 49.7173 Evaluate side-chains 134 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 70 ILE Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 230 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 165 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 97 optimal weight: 0.9990 chunk 125 optimal weight: 9.9990 chunk 96 optimal weight: 0.0470 chunk 144 optimal weight: 0.4980 chunk 95 optimal weight: 0.8980 chunk 170 optimal weight: 0.3980 chunk 106 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14780 Z= 0.119 Angle : 0.427 8.778 19911 Z= 0.226 Chirality : 0.038 0.148 2268 Planarity : 0.002 0.038 2479 Dihedral : 10.400 160.849 1996 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 1.40 % Allowed : 14.13 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1791 helix: 1.73 (0.17), residues: 1027 sheet: -0.10 (0.39), residues: 189 loop : -1.36 (0.25), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 605 HIS 0.002 0.000 HIS B 202 PHE 0.013 0.001 PHE D 52 TYR 0.015 0.001 TYR C 134 ARG 0.002 0.000 ARG C 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 111 time to evaluate : 1.609 Fit side-chains revert: symmetry clash REVERT: A 376 MET cc_start: -0.0722 (pmm) cc_final: -0.1196 (mmm) REVERT: A 607 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.8015 (pp) REVERT: B 221 MET cc_start: 0.7352 (OUTLIER) cc_final: 0.6102 (mmt) REVERT: C 3 ILE cc_start: 0.7457 (tt) cc_final: 0.7089 (tt) REVERT: C 69 ASN cc_start: 0.8504 (OUTLIER) cc_final: 0.8168 (m-40) REVERT: D 100 HIS cc_start: 0.5255 (t-90) cc_final: 0.4850 (t-170) outliers start: 22 outliers final: 15 residues processed: 127 average time/residue: 0.2668 time to fit residues: 50.8911 Evaluate side-chains 131 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 93 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 105 optimal weight: 0.8980 chunk 68 optimal weight: 0.0060 chunk 101 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 108 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 84 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 155 optimal weight: 5.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN D 162 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14780 Z= 0.124 Angle : 0.422 7.369 19911 Z= 0.223 Chirality : 0.039 0.153 2268 Planarity : 0.003 0.037 2479 Dihedral : 10.256 161.742 1996 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.15 % Allowed : 14.32 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1791 helix: 1.79 (0.17), residues: 1027 sheet: -0.11 (0.39), residues: 191 loop : -1.33 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 605 HIS 0.002 0.000 HIS C 160 PHE 0.012 0.001 PHE D 52 TYR 0.012 0.001 TYR A 164 ARG 0.001 0.000 ARG C 232 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 111 time to evaluate : 1.629 Fit side-chains REVERT: A 376 MET cc_start: -0.0741 (pmm) cc_final: -0.1127 (mmm) REVERT: A 416 MET cc_start: -0.0080 (tpp) cc_final: -0.0318 (tpp) REVERT: A 607 LEU cc_start: 0.8298 (OUTLIER) cc_final: 0.8007 (pp) REVERT: B 221 MET cc_start: 0.7405 (OUTLIER) cc_final: 0.6105 (mmt) REVERT: C 69 ASN cc_start: 0.8520 (OUTLIER) cc_final: 0.8149 (m-40) REVERT: D 100 HIS cc_start: 0.5276 (t-90) cc_final: 0.4889 (t70) outliers start: 18 outliers final: 14 residues processed: 125 average time/residue: 0.2659 time to fit residues: 50.1833 Evaluate side-chains 128 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 111 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 163 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 158 optimal weight: 9.9990 chunk 95 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 124 optimal weight: 20.0000 chunk 48 optimal weight: 4.9990 chunk 143 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 104 optimal weight: 0.5980 chunk 168 optimal weight: 10.0000 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14780 Z= 0.202 Angle : 0.471 7.756 19911 Z= 0.248 Chirality : 0.040 0.167 2268 Planarity : 0.003 0.036 2479 Dihedral : 10.299 159.807 1996 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.46 % Allowed : 14.19 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1791 helix: 1.67 (0.17), residues: 1027 sheet: -0.28 (0.39), residues: 193 loop : -1.37 (0.25), residues: 571 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 605 HIS 0.005 0.001 HIS B 202 PHE 0.013 0.001 PHE A 160 TYR 0.016 0.001 TYR A 164 ARG 0.002 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 113 time to evaluate : 1.703 Fit side-chains REVERT: A 376 MET cc_start: -0.0834 (pmm) cc_final: -0.1050 (mmm) REVERT: A 416 MET cc_start: 0.0059 (tpp) cc_final: -0.0204 (tpp) REVERT: A 607 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.8099 (pp) REVERT: C 69 ASN cc_start: 0.8532 (OUTLIER) cc_final: 0.8152 (m-40) REVERT: D 100 HIS cc_start: 0.5305 (t-90) cc_final: 0.4894 (t70) outliers start: 23 outliers final: 19 residues processed: 130 average time/residue: 0.2623 time to fit residues: 51.2031 Evaluate side-chains 132 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 9 ILE Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain D residue 308 VAL Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 102 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 116 optimal weight: 0.7980 chunk 176 optimal weight: 0.5980 chunk 162 optimal weight: 0.2980 chunk 140 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 108 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 111 optimal weight: 3.9990 chunk 149 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 233 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 14780 Z= 0.128 Angle : 0.435 8.695 19911 Z= 0.227 Chirality : 0.039 0.156 2268 Planarity : 0.003 0.037 2479 Dihedral : 10.128 160.401 1996 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.21 % Allowed : 14.64 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1791 helix: 1.77 (0.17), residues: 1027 sheet: -0.06 (0.39), residues: 191 loop : -1.34 (0.25), residues: 573 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 605 HIS 0.003 0.000 HIS C 160 PHE 0.012 0.001 PHE D 52 TYR 0.012 0.001 TYR A 623 ARG 0.001 0.000 ARG A 513 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3582 Ramachandran restraints generated. 1791 Oldfield, 0 Emsley, 1791 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 1.629 Fit side-chains REVERT: A 416 MET cc_start: -0.0067 (tpp) cc_final: -0.0323 (tpp) REVERT: A 607 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.8067 (pp) REVERT: B 221 MET cc_start: 0.7424 (OUTLIER) cc_final: 0.6293 (mmt) REVERT: C 69 ASN cc_start: 0.8519 (OUTLIER) cc_final: 0.8146 (m-40) REVERT: D 100 HIS cc_start: 0.5264 (t-90) cc_final: 0.4868 (t70) outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.2690 time to fit residues: 49.9785 Evaluate side-chains 127 residues out of total 1571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 109 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 423 VAL Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 601 VAL Chi-restraints excluded: chain A residue 607 LEU Chi-restraints excluded: chain A residue 618 MET Chi-restraints excluded: chain B residue 75 LYS Chi-restraints excluded: chain B residue 94 TYR Chi-restraints excluded: chain B residue 221 MET Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 69 ASN Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain D residue 124 HIS Chi-restraints excluded: chain D residue 125 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 308 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 177 random chunks: chunk 43 optimal weight: 6.9990 chunk 129 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 140 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 144 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 498 ASN A 502 GLN C 233 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.217830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.149576 restraints weight = 18633.229| |-----------------------------------------------------------------------------| r_work (start): 0.3639 rms_B_bonded: 9.59 r_work: 0.3127 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14780 Z= 0.245 Angle : 0.505 7.915 19911 Z= 0.263 Chirality : 0.041 0.178 2268 Planarity : 0.003 0.036 2479 Dihedral : 10.293 158.993 1996 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 1.65 % Allowed : 14.39 % Favored : 83.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1791 helix: 1.61 (0.17), residues: 1024 sheet: -0.25 (0.39), residues: 193 loop : -1.35 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 605 HIS 0.005 0.001 HIS B 202 PHE 0.014 0.001 PHE A 524 TYR 0.017 0.002 TYR A 164 ARG 0.002 0.000 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2949.41 seconds wall clock time: 54 minutes 30.94 seconds (3270.94 seconds total)