Starting phenix.real_space_refine on Sun Jun 8 04:52:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7c_61201/06_2025/9j7c_61201_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7c_61201/06_2025/9j7c_61201.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7c_61201/06_2025/9j7c_61201.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7c_61201/06_2025/9j7c_61201.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7c_61201/06_2025/9j7c_61201_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7c_61201/06_2025/9j7c_61201_neut.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 40 5.16 5 C 6152 2.51 5 N 1480 2.21 5 O 1580 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9252 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4500 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 19, 'TRANS': 576} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 596, 4500 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 19, 'TRANS': 576} Chain breaks: 3 bond proxies already assigned to first conformer: 4581 Chain: "B" Number of atoms: 4526 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 596, 4500 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 19, 'TRANS': 576} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 596, 4500 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 19, 'TRANS': 576} Chain breaks: 3 bond proxies already assigned to first conformer: 4581 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 90 Unusual residues: {'R16': 1, 'URE': 1, 'Y01': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 104 Unusual residues: {'C14': 1, 'R16': 1, 'URE': 1, 'Y01': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N ATRP A 95 " occ=0.56 ... (26 atoms not shown) pdb=" CH2BTRP A 95 " occ=0.44 residue: pdb=" N ATYR A 315 " occ=0.52 ... (22 atoms not shown) pdb=" OH BTYR A 315 " occ=0.48 residue: pdb=" N ATRP B 95 " occ=0.56 ... (26 atoms not shown) pdb=" CH2BTRP B 95 " occ=0.44 residue: pdb=" N ATYR B 315 " occ=0.52 ... (22 atoms not shown) pdb=" OH BTYR B 315 " occ=0.48 Time building chain proxies: 11.97, per 1000 atoms: 1.29 Number of scatterers: 9252 At special positions: 0 Unit cell: (116.45, 87.55, 91.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 40 16.00 O 1580 8.00 N 1480 7.00 C 6152 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 264 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 264 " - pdb=" SG CYS B 275 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 2.4 seconds 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2148 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 71.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 34 through 42 removed outlier: 3.619A pdb=" N GLY A 38 " --> pdb=" O ASP A 34 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 56 removed outlier: 3.534A pdb=" N SER A 54 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 56 " --> pdb=" O PHE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 94 removed outlier: 3.759A pdb=" N VAL A 88 " --> pdb=" O LEU A 84 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLN A 92 " --> pdb=" O VAL A 88 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TRP A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 108 removed outlier: 4.359A pdb=" N ILE A 99 " --> pdb=" O ATRP A 95 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU A 100 " --> pdb=" O ALA A 96 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER A 102 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 119 removed outlier: 4.129A pdb=" N PHE A 115 " --> pdb=" O VAL A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 139 removed outlier: 3.541A pdb=" N MET A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU A 134 " --> pdb=" O VAL A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 153 removed outlier: 3.516A pdb=" N VAL A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS A 150 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA A 151 " --> pdb=" O GLU A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 175 removed outlier: 3.705A pdb=" N PHE A 161 " --> pdb=" O THR A 157 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 166 " --> pdb=" O LEU A 162 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR A 168 " --> pdb=" O PHE A 164 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 169 " --> pdb=" O CYS A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 188 removed outlier: 3.595A pdb=" N SER A 181 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 182 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 209 removed outlier: 4.088A pdb=" N PHE A 197 " --> pdb=" O TYR A 193 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU A 198 " --> pdb=" O ALA A 194 " (cutoff:3.500A) Proline residue: A 200 - end of helix removed outlier: 3.739A pdb=" N TYR A 206 " --> pdb=" O GLY A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 238 removed outlier: 3.727A pdb=" N VAL A 221 " --> pdb=" O LEU A 217 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 225 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 226 " --> pdb=" O HIS A 222 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS A 227 " --> pdb=" O SER A 223 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N VAL A 231 " --> pdb=" O HIS A 227 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL A 237 " --> pdb=" O PHE A 233 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 258 removed outlier: 3.712A pdb=" N VAL A 250 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR A 251 " --> pdb=" O PRO A 247 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL A 258 " --> pdb=" O LEU A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 285 removed outlier: 3.593A pdb=" N SER A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 310 removed outlier: 3.573A pdb=" N GLY A 298 " --> pdb=" O GLY A 294 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEU A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY A 307 " --> pdb=" O VAL A 303 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR A 308 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 309 " --> pdb=" O ASN A 305 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE A 310 " --> pdb=" O PHE A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 Processing helix chain 'A' and resid 339 through 350 removed outlier: 3.681A pdb=" N PHE A 343 " --> pdb=" O PHE A 339 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU A 345 " --> pdb=" O VAL A 341 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA A 346 " --> pdb=" O PRO A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.831A pdb=" N LEU A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 368 Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.572A pdb=" N LEU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA A 394 " --> pdb=" O MET A 390 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER A 397 " --> pdb=" O MET A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 412 removed outlier: 3.615A pdb=" N LEU A 403 " --> pdb=" O GLY A 399 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER A 408 " --> pdb=" O ILE A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 426 through 454 removed outlier: 3.518A pdb=" N LYS A 430 " --> pdb=" O ARG A 426 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA A 435 " --> pdb=" O ILE A 431 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY A 438 " --> pdb=" O CYS A 434 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE A 439 " --> pdb=" O ALA A 435 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA A 453 " --> pdb=" O VAL A 449 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLY A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 469 removed outlier: 3.555A pdb=" N LEU A 467 " --> pdb=" O ALA A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 481 removed outlier: 3.770A pdb=" N MET A 478 " --> pdb=" O PRO A 474 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 479 " --> pdb=" O ILE A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 513 removed outlier: 3.507A pdb=" N ALA A 489 " --> pdb=" O ASN A 485 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 496 " --> pdb=" O GLY A 492 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS A 497 " --> pdb=" O ALA A 493 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL A 498 " --> pdb=" O THR A 494 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR A 503 " --> pdb=" O PHE A 499 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 508 " --> pdb=" O TRP A 504 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N LYS A 509 " --> pdb=" O LEU A 505 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 521 removed outlier: 3.860A pdb=" N GLY A 521 " --> pdb=" O LEU A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 544 removed outlier: 3.585A pdb=" N MET A 526 " --> pdb=" O LYS A 522 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 527 " --> pdb=" O ASN A 523 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 528 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 538 " --> pdb=" O ILE A 534 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 541 " --> pdb=" O GLY A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 605 removed outlier: 4.382A pdb=" N LYS A 589 " --> pdb=" O LEU A 585 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 594 " --> pdb=" O ALA A 590 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU A 597 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N PHE A 599 " --> pdb=" O TRP A 595 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL A 605 " --> pdb=" O ILE A 601 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 612 removed outlier: 3.558A pdb=" N SER A 611 " --> pdb=" O TRP A 607 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU A 612 " --> pdb=" O PRO A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 615 No H-bonds generated for 'chain 'A' and resid 613 through 615' Processing helix chain 'A' and resid 621 through 636 removed outlier: 3.735A pdb=" N ILE A 630 " --> pdb=" O ALA A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 642 through 646 Processing helix chain 'B' and resid 34 through 42 removed outlier: 3.619A pdb=" N GLY B 38 " --> pdb=" O ASP B 34 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 42 " --> pdb=" O GLY B 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 56 removed outlier: 3.533A pdb=" N SER B 54 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 56 " --> pdb=" O PHE B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 94 removed outlier: 3.759A pdb=" N VAL B 88 " --> pdb=" O LEU B 84 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN B 92 " --> pdb=" O VAL B 88 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP B 93 " --> pdb=" O ILE B 89 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR B 94 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 108 removed outlier: 4.358A pdb=" N ILE B 99 " --> pdb=" O ATRP B 95 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU B 100 " --> pdb=" O ALA B 96 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N SER B 102 " --> pdb=" O THR B 98 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N SER B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLN B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 119 removed outlier: 4.129A pdb=" N PHE B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 139 removed outlier: 3.541A pdb=" N MET B 131 " --> pdb=" O LEU B 127 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLU B 134 " --> pdb=" O VAL B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 153 removed outlier: 3.516A pdb=" N VAL B 149 " --> pdb=" O VAL B 145 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LYS B 150 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA B 151 " --> pdb=" O GLU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 175 removed outlier: 3.705A pdb=" N PHE B 161 " --> pdb=" O THR B 157 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 166 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N THR B 168 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN B 169 " --> pdb=" O CYS B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 188 removed outlier: 3.596A pdb=" N SER B 181 " --> pdb=" O LEU B 177 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 182 " --> pdb=" O LEU B 178 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASN B 185 " --> pdb=" O SER B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 209 removed outlier: 4.088A pdb=" N PHE B 197 " --> pdb=" O TYR B 193 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LEU B 198 " --> pdb=" O ALA B 194 " (cutoff:3.500A) Proline residue: B 200 - end of helix removed outlier: 3.739A pdb=" N TYR B 206 " --> pdb=" O GLY B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 238 removed outlier: 3.727A pdb=" N VAL B 221 " --> pdb=" O LEU B 217 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N HIS B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N SER B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 225 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL B 226 " --> pdb=" O HIS B 222 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N HIS B 227 " --> pdb=" O SER B 223 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N VAL B 231 " --> pdb=" O HIS B 227 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL B 237 " --> pdb=" O PHE B 233 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TYR B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 258 removed outlier: 3.713A pdb=" N VAL B 250 " --> pdb=" O SER B 246 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N TYR B 251 " --> pdb=" O PRO B 247 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASP B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP B 256 " --> pdb=" O ASP B 252 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET B 257 " --> pdb=" O ARG B 253 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N VAL B 258 " --> pdb=" O LEU B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 285 removed outlier: 3.594A pdb=" N SER B 285 " --> pdb=" O PHE B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 310 removed outlier: 3.572A pdb=" N GLY B 298 " --> pdb=" O GLY B 294 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 299 " --> pdb=" O ALA B 295 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N GLY B 307 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 308 " --> pdb=" O GLY B 304 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL B 309 " --> pdb=" O ASN B 305 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N PHE B 310 " --> pdb=" O PHE B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 321 Processing helix chain 'B' and resid 339 through 350 removed outlier: 3.681A pdb=" N PHE B 343 " --> pdb=" O PHE B 339 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 345 " --> pdb=" O VAL B 341 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 346 " --> pdb=" O PRO B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 350 through 356 removed outlier: 3.832A pdb=" N LEU B 354 " --> pdb=" O GLY B 350 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA B 355 " --> pdb=" O LEU B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 368 Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 382 through 399 removed outlier: 3.572A pdb=" N LEU B 386 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA B 394 " --> pdb=" O MET B 390 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER B 397 " --> pdb=" O MET B 393 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 412 removed outlier: 3.616A pdb=" N LEU B 403 " --> pdb=" O GLY B 399 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER B 408 " --> pdb=" O ILE B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 454 removed outlier: 3.518A pdb=" N LYS B 430 " --> pdb=" O ARG B 426 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ALA B 435 " --> pdb=" O ILE B 431 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL B 436 " --> pdb=" O SER B 432 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU B 437 " --> pdb=" O ARG B 433 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY B 438 " --> pdb=" O CYS B 434 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE B 439 " --> pdb=" O ALA B 435 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLY B 444 " --> pdb=" O GLY B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.554A pdb=" N LEU B 467 " --> pdb=" O ALA B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.771A pdb=" N MET B 478 " --> pdb=" O PRO B 474 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 485 through 513 removed outlier: 3.508A pdb=" N ALA B 489 " --> pdb=" O ASN B 485 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLY B 496 " --> pdb=" O GLY B 492 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N CYS B 497 " --> pdb=" O ALA B 493 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N VAL B 498 " --> pdb=" O THR B 494 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N THR B 503 " --> pdb=" O PHE B 499 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA B 508 " --> pdb=" O TRP B 504 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LYS B 509 " --> pdb=" O LEU B 505 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 521 removed outlier: 3.860A pdb=" N GLY B 521 " --> pdb=" O LEU B 517 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 544 removed outlier: 3.585A pdb=" N MET B 526 " --> pdb=" O LYS B 522 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU B 527 " --> pdb=" O ASN B 523 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA B 528 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY B 537 " --> pdb=" O ALA B 533 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY B 538 " --> pdb=" O ILE B 534 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS B 541 " --> pdb=" O GLY B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 583 through 605 removed outlier: 4.382A pdb=" N LYS B 589 " --> pdb=" O LEU B 585 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS B 594 " --> pdb=" O ALA B 590 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N LEU B 597 " --> pdb=" O VAL B 593 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE B 599 " --> pdb=" O TRP B 595 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N VAL B 605 " --> pdb=" O ILE B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 612 removed outlier: 3.558A pdb=" N SER B 611 " --> pdb=" O TRP B 607 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LEU B 612 " --> pdb=" O PRO B 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 615 No H-bonds generated for 'chain 'B' and resid 613 through 615' Processing helix chain 'B' and resid 621 through 636 removed outlier: 3.735A pdb=" N ILE B 630 " --> pdb=" O ALA B 626 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 2.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1352 1.31 - 1.43: 2694 1.43 - 1.56: 5377 1.56 - 1.69: 0 1.69 - 1.82: 64 Bond restraints: 9487 Sorted by residual: bond pdb=" CA SER A 456 " pdb=" CB SER A 456 " ideal model delta sigma weight residual 1.534 1.427 0.107 1.72e-02 3.38e+03 3.86e+01 bond pdb=" CA SER B 456 " pdb=" CB SER B 456 " ideal model delta sigma weight residual 1.534 1.427 0.106 1.72e-02 3.38e+03 3.83e+01 bond pdb=" C SER A 456 " pdb=" O SER A 456 " ideal model delta sigma weight residual 1.234 1.184 0.051 1.11e-02 8.12e+03 2.10e+01 bond pdb=" C SER B 456 " pdb=" O SER B 456 " ideal model delta sigma weight residual 1.234 1.184 0.050 1.11e-02 8.12e+03 2.06e+01 bond pdb=" C PRO A 267 " pdb=" O PRO A 267 " ideal model delta sigma weight residual 1.239 1.184 0.055 1.22e-02 6.72e+03 2.05e+01 ... (remaining 9482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.54: 12620 2.54 - 5.08: 269 5.08 - 7.62: 43 7.62 - 10.16: 6 10.16 - 12.70: 4 Bond angle restraints: 12942 Sorted by residual: angle pdb=" N TRP B 459 " pdb=" CA TRP B 459 " pdb=" C TRP B 459 " ideal model delta sigma weight residual 113.55 100.85 12.70 1.26e+00 6.30e-01 1.02e+02 angle pdb=" N TRP A 459 " pdb=" CA TRP A 459 " pdb=" C TRP A 459 " ideal model delta sigma weight residual 112.93 102.69 10.24 1.33e+00 5.65e-01 5.93e+01 angle pdb=" N LEU B 457 " pdb=" CA LEU B 457 " pdb=" C LEU B 457 " ideal model delta sigma weight residual 110.35 101.00 9.35 1.40e+00 5.10e-01 4.46e+01 angle pdb=" N LEU A 457 " pdb=" CA LEU A 457 " pdb=" C LEU A 457 " ideal model delta sigma weight residual 110.35 101.01 9.34 1.40e+00 5.10e-01 4.45e+01 angle pdb=" N GLY B 458 " pdb=" CA GLY B 458 " pdb=" C GLY B 458 " ideal model delta sigma weight residual 113.58 107.26 6.32 1.07e+00 8.73e-01 3.49e+01 ... (remaining 12937 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 4699 14.03 - 28.06: 606 28.06 - 42.09: 210 42.09 - 56.12: 60 56.12 - 70.16: 18 Dihedral angle restraints: 5593 sinusoidal: 2211 harmonic: 3382 Sorted by residual: dihedral pdb=" CD ARG B 262 " pdb=" NE ARG B 262 " pdb=" CZ ARG B 262 " pdb=" NH1 ARG B 262 " ideal model delta sinusoidal sigma weight residual 0.00 -70.16 70.16 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" CD ARG A 262 " pdb=" NE ARG A 262 " pdb=" CZ ARG A 262 " pdb=" NH1 ARG A 262 " ideal model delta sinusoidal sigma weight residual 0.00 -70.15 70.15 1 1.00e+01 1.00e-02 6.34e+01 dihedral pdb=" N LEU A 457 " pdb=" C LEU A 457 " pdb=" CA LEU A 457 " pdb=" CB LEU A 457 " ideal model delta harmonic sigma weight residual 122.80 109.67 13.13 0 2.50e+00 1.60e-01 2.76e+01 ... (remaining 5590 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 1407 0.077 - 0.155: 114 0.155 - 0.232: 13 0.232 - 0.309: 2 0.309 - 0.387: 2 Chirality restraints: 1538 Sorted by residual: chirality pdb=" CA LEU B 457 " pdb=" N LEU B 457 " pdb=" C LEU B 457 " pdb=" CB LEU B 457 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.74e+00 chirality pdb=" CA LEU A 457 " pdb=" N LEU A 457 " pdb=" C LEU A 457 " pdb=" CB LEU A 457 " both_signs ideal model delta sigma weight residual False 2.51 2.89 -0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB VAL A 646 " pdb=" CA VAL A 646 " pdb=" CG1 VAL A 646 " pdb=" CG2 VAL A 646 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 ... (remaining 1535 not shown) Planarity restraints: 1538 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 262 " -1.020 9.50e-02 1.11e+02 4.57e-01 1.26e+02 pdb=" NE ARG A 262 " 0.062 2.00e-02 2.50e+03 pdb=" CZ ARG A 262 " 0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 262 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 262 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 262 " 1.019 9.50e-02 1.11e+02 4.57e-01 1.26e+02 pdb=" NE ARG B 262 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG B 262 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 262 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 262 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 514 " -0.645 9.50e-02 1.11e+02 2.89e-01 5.09e+01 pdb=" NE ARG B 514 " 0.038 2.00e-02 2.50e+03 pdb=" CZ ARG B 514 " 0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG B 514 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 514 " -0.021 2.00e-02 2.50e+03 ... (remaining 1535 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1814 2.77 - 3.30: 8252 3.30 - 3.83: 14145 3.83 - 4.37: 17526 4.37 - 4.90: 31260 Nonbonded interactions: 72997 Sorted by model distance: nonbonded pdb=" OD1 ASN B 281 " pdb=" OG SER B 291 " model vdw 2.235 3.040 nonbonded pdb=" OD1 ASN A 281 " pdb=" OG SER A 291 " model vdw 2.235 3.040 nonbonded pdb=" O MET B 526 " pdb=" ND2 ASN B 530 " model vdw 2.245 3.120 nonbonded pdb=" O MET A 526 " pdb=" ND2 ASN A 530 " model vdw 2.245 3.120 nonbonded pdb=" OG1 THR B 98 " pdb=" O URE B 805 " model vdw 2.314 3.040 ... (remaining 72992 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 94 or resid 96 through 314 or resid 316 through \ 648 or resid 801)) selection = (chain 'B' and (resid 5 through 94 or resid 96 through 314 or resid 316 through \ 648 or resid 801)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.44 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.620 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 32.540 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.070 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:15.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.005 0.107 9489 Z= 0.322 Angle : 0.888 12.695 12946 Z= 0.565 Chirality : 0.050 0.387 1538 Planarity : 0.021 0.457 1538 Dihedral : 15.069 70.156 3439 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.87 % Favored : 93.79 % Rotamer: Outliers : 0.63 % Allowed : 22.84 % Favored : 76.53 % Cbeta Deviations : 0.37 % 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: -4.19 (0.21), residues: 1188 helix: -2.42 (0.16), residues: 814 sheet: None (None), residues: 0 loop : -3.24 (0.26), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 504 HIS 0.003 0.001 HIS B 541 PHE 0.026 0.002 PHE A 306 TYR 0.008 0.001 TYR B 512 ARG 0.003 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.25050 ( 412) hydrogen bonds : angle 7.98979 ( 1224) SS BOND : bond 0.00072 ( 2) SS BOND : angle 1.09745 ( 4) covalent geometry : bond 0.00545 ( 9487) covalent geometry : angle 0.88779 (12942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.919 Fit side-chains REVERT: B 127 LEU cc_start: 0.8794 (mt) cc_final: 0.8519 (mm) outliers start: 6 outliers final: 3 residues processed: 106 average time/residue: 0.9954 time to fit residues: 114.8044 Evaluate side-chains 68 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 457 LEU Chi-restraints excluded: chain B residue 580 LEU Chi-restraints excluded: chain B residue 647 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.5980 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 56 optimal weight: 0.0070 chunk 68 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.156493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.130525 restraints weight = 59319.930| |-----------------------------------------------------------------------------| r_work (start): 0.3627 rms_B_bonded: 6.46 r_work: 0.3286 rms_B_bonded: 6.25 restraints_weight: 2.0000 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3299 r_free = 0.3299 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3299 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9489 Z= 0.129 Angle : 0.622 8.134 12946 Z= 0.318 Chirality : 0.041 0.233 1538 Planarity : 0.005 0.066 1538 Dihedral : 7.885 79.049 1602 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 3.16 % Allowed : 22.00 % Favored : 74.84 % 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: -3.33 (0.22), residues: 1188 helix: -1.74 (0.17), residues: 834 sheet: None (None), residues: 0 loop : -3.03 (0.28), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 504 HIS 0.003 0.001 HIS B 158 PHE 0.015 0.001 PHE B 392 TYR 0.007 0.001 TYR B 552 ARG 0.006 0.001 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04249 ( 412) hydrogen bonds : angle 4.76969 ( 1224) SS BOND : bond 0.00539 ( 2) SS BOND : angle 1.34166 ( 4) covalent geometry : bond 0.00281 ( 9487) covalent geometry : angle 0.62119 (12942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 79 time to evaluate : 1.009 Fit side-chains REVERT: A 318 SER cc_start: 0.8272 (p) cc_final: 0.8060 (m) outliers start: 29 outliers final: 14 residues processed: 98 average time/residue: 0.8157 time to fit residues: 88.5854 Evaluate side-chains 84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 609 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 85 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 0.1980 chunk 117 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.149333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.123623 restraints weight = 51858.929| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 5.73 r_work: 0.3228 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3241 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9489 Z= 0.136 Angle : 0.624 9.047 12946 Z= 0.314 Chirality : 0.041 0.222 1538 Planarity : 0.005 0.061 1538 Dihedral : 7.401 59.667 1595 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.51 % Favored : 95.41 % Rotamer: Outliers : 3.16 % Allowed : 22.32 % Favored : 74.53 % 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: -2.74 (0.23), residues: 1188 helix: -1.30 (0.17), residues: 838 sheet: None (None), residues: 0 loop : -2.80 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 504 HIS 0.003 0.001 HIS B 158 PHE 0.012 0.001 PHE A 392 TYR 0.008 0.001 TYR B 512 ARG 0.018 0.001 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.05054 ( 412) hydrogen bonds : angle 4.50515 ( 1224) SS BOND : bond 0.00034 ( 2) SS BOND : angle 0.76930 ( 4) covalent geometry : bond 0.00319 ( 9487) covalent geometry : angle 0.62346 (12942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.018 Fit side-chains REVERT: A 514 ARG cc_start: 0.8500 (pmt-80) cc_final: 0.8123 (pmt-80) REVERT: B 263 SER cc_start: 0.8735 (OUTLIER) cc_final: 0.8526 (p) REVERT: B 323 ARG cc_start: 0.6940 (ptp-110) cc_final: 0.6268 (mmm-85) outliers start: 28 outliers final: 15 residues processed: 95 average time/residue: 0.8455 time to fit residues: 88.9041 Evaluate side-chains 83 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 265 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 91 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 263 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 269 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 426 ARG Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 78 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 21 optimal weight: 0.0050 chunk 47 optimal weight: 0.5980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.150192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.124811 restraints weight = 57074.146| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 6.21 r_work: 0.3234 rms_B_bonded: 5.52 restraints_weight: 2.0000 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9489 Z= 0.113 Angle : 0.575 8.717 12946 Z= 0.287 Chirality : 0.040 0.196 1538 Planarity : 0.005 0.062 1538 Dihedral : 7.183 58.037 1595 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.42 % Favored : 95.49 % Rotamer: Outliers : 2.53 % Allowed : 21.89 % Favored : 75.58 % 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: -2.42 (0.23), residues: 1188 helix: -1.04 (0.18), residues: 838 sheet: None (None), residues: 0 loop : -2.74 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 504 HIS 0.002 0.001 HIS A 227 PHE 0.012 0.001 PHE A 392 TYR 0.008 0.001 TYR B 220 ARG 0.008 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03841 ( 412) hydrogen bonds : angle 4.36601 ( 1224) SS BOND : bond 0.00081 ( 2) SS BOND : angle 0.90931 ( 4) covalent geometry : bond 0.00267 ( 9487) covalent geometry : angle 0.57462 (12942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 1.006 Fit side-chains REVERT: A 426 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6662 (tpp-160) REVERT: A 514 ARG cc_start: 0.8477 (pmt-80) cc_final: 0.8122 (pmt-80) REVERT: B 131 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8628 (ptp) outliers start: 22 outliers final: 13 residues processed: 88 average time/residue: 1.1720 time to fit residues: 112.7171 Evaluate side-chains 83 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 68 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 110 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 92 optimal weight: 0.9990 chunk 107 optimal weight: 0.0970 chunk 117 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.148072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.122128 restraints weight = 46072.984| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 5.05 r_work: 0.3228 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9489 Z= 0.130 Angle : 0.603 9.856 12946 Z= 0.300 Chirality : 0.041 0.268 1538 Planarity : 0.005 0.068 1538 Dihedral : 7.244 59.086 1595 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 3.05 % Allowed : 21.47 % Favored : 75.47 % 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: -2.23 (0.24), residues: 1188 helix: -0.90 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -2.69 (0.30), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 504 HIS 0.003 0.001 HIS A 541 PHE 0.013 0.001 PHE B 392 TYR 0.006 0.001 TYR B 220 ARG 0.012 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.04406 ( 412) hydrogen bonds : angle 4.35537 ( 1224) SS BOND : bond 0.00028 ( 2) SS BOND : angle 0.61884 ( 4) covalent geometry : bond 0.00306 ( 9487) covalent geometry : angle 0.60311 (12942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 71 time to evaluate : 1.048 Fit side-chains REVERT: A 426 ARG cc_start: 0.6828 (OUTLIER) cc_final: 0.6584 (tpp-160) REVERT: A 514 ARG cc_start: 0.8479 (pmt-80) cc_final: 0.8225 (pmt-80) REVERT: B 131 MET cc_start: 0.8784 (OUTLIER) cc_final: 0.8583 (ptp) outliers start: 27 outliers final: 18 residues processed: 92 average time/residue: 0.9465 time to fit residues: 95.8408 Evaluate side-chains 90 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 131 MET Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 265 THR Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 27 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 116 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.119650 restraints weight = 55131.348| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 5.77 r_work: 0.3161 rms_B_bonded: 5.49 restraints_weight: 2.0000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3176 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9489 Z= 0.168 Angle : 0.638 10.606 12946 Z= 0.319 Chirality : 0.043 0.230 1538 Planarity : 0.005 0.062 1538 Dihedral : 7.428 59.632 1595 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 3.26 % Allowed : 21.05 % Favored : 75.68 % 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: -2.33 (0.23), residues: 1188 helix: -0.96 (0.18), residues: 842 sheet: None (None), residues: 0 loop : -2.74 (0.30), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 504 HIS 0.003 0.001 HIS A 541 PHE 0.016 0.002 PHE A 392 TYR 0.007 0.001 TYR B 512 ARG 0.012 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 412) hydrogen bonds : angle 4.44995 ( 1224) SS BOND : bond 0.00057 ( 2) SS BOND : angle 1.07016 ( 4) covalent geometry : bond 0.00411 ( 9487) covalent geometry : angle 0.63827 (12942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 69 time to evaluate : 0.972 Fit side-chains REVERT: A 426 ARG cc_start: 0.6912 (OUTLIER) cc_final: 0.6653 (tpp-160) REVERT: A 514 ARG cc_start: 0.8484 (pmt-80) cc_final: 0.8126 (pmt-80) outliers start: 29 outliers final: 17 residues processed: 90 average time/residue: 1.1614 time to fit residues: 115.7894 Evaluate side-chains 82 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 64 time to evaluate : 1.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.5980 chunk 107 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 112 optimal weight: 5.9990 chunk 34 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 420 ASN B 222 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.122564 restraints weight = 57553.101| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 5.92 r_work: 0.3192 rms_B_bonded: 5.78 restraints_weight: 2.0000 r_work (final): 0.3192 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3211 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3211 r_free = 0.3211 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3211 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9489 Z= 0.113 Angle : 0.585 9.975 12946 Z= 0.290 Chirality : 0.040 0.219 1538 Planarity : 0.005 0.061 1538 Dihedral : 7.154 59.884 1595 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.42 % Allowed : 22.00 % Favored : 75.58 % 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: -2.00 (0.24), residues: 1188 helix: -0.67 (0.18), residues: 834 sheet: None (None), residues: 0 loop : -2.72 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 625 HIS 0.003 0.001 HIS A 541 PHE 0.012 0.001 PHE B 392 TYR 0.007 0.001 TYR B 220 ARG 0.014 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.04045 ( 412) hydrogen bonds : angle 4.33399 ( 1224) SS BOND : bond 0.00022 ( 2) SS BOND : angle 0.79936 ( 4) covalent geometry : bond 0.00262 ( 9487) covalent geometry : angle 0.58487 (12942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 67 time to evaluate : 1.246 Fit side-chains REVERT: A 426 ARG cc_start: 0.6903 (OUTLIER) cc_final: 0.6650 (tpp-160) REVERT: A 514 ARG cc_start: 0.8460 (pmt-80) cc_final: 0.8210 (pmt-80) outliers start: 21 outliers final: 15 residues processed: 84 average time/residue: 1.1098 time to fit residues: 102.3804 Evaluate side-chains 79 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 83 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 0.4980 chunk 28 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119051 restraints weight = 51498.608| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 5.69 r_work: 0.3151 rms_B_bonded: 5.21 restraints_weight: 2.0000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9489 Z= 0.195 Angle : 0.667 11.510 12946 Z= 0.333 Chirality : 0.045 0.269 1538 Planarity : 0.005 0.061 1538 Dihedral : 7.339 57.640 1595 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 2.84 % Allowed : 21.79 % Favored : 75.37 % 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: -2.26 (0.23), residues: 1188 helix: -0.89 (0.17), residues: 846 sheet: None (None), residues: 0 loop : -2.81 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 504 HIS 0.003 0.001 HIS A 541 PHE 0.017 0.002 PHE B 48 TYR 0.010 0.001 TYR B 512 ARG 0.013 0.001 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.05573 ( 412) hydrogen bonds : angle 4.47931 ( 1224) SS BOND : bond 0.00076 ( 2) SS BOND : angle 1.02653 ( 4) covalent geometry : bond 0.00486 ( 9487) covalent geometry : angle 0.66640 (12942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 64 time to evaluate : 1.121 Fit side-chains REVERT: A 426 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6657 (tpp-160) REVERT: A 514 ARG cc_start: 0.8475 (pmt-80) cc_final: 0.8130 (pmt-80) REVERT: B 559 GLU cc_start: 0.8519 (mt-10) cc_final: 0.8187 (pp20) outliers start: 25 outliers final: 21 residues processed: 83 average time/residue: 1.5740 time to fit residues: 144.5920 Evaluate side-chains 84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 460 MET Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 45 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 108 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.143950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.118755 restraints weight = 49743.902| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 5.38 r_work: 0.3161 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9489 Z= 0.187 Angle : 0.658 11.587 12946 Z= 0.328 Chirality : 0.044 0.258 1538 Planarity : 0.005 0.061 1538 Dihedral : 7.223 54.457 1595 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.63 % Allowed : 21.89 % Favored : 75.47 % 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: -2.22 (0.23), residues: 1188 helix: -0.85 (0.18), residues: 840 sheet: None (None), residues: 0 loop : -2.81 (0.29), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 504 HIS 0.004 0.001 HIS A 541 PHE 0.018 0.002 PHE B 48 TYR 0.010 0.001 TYR B 512 ARG 0.015 0.001 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.05380 ( 412) hydrogen bonds : angle 4.50144 ( 1224) SS BOND : bond 0.00063 ( 2) SS BOND : angle 1.35838 ( 4) covalent geometry : bond 0.00466 ( 9487) covalent geometry : angle 0.65752 (12942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 64 time to evaluate : 0.896 Fit side-chains REVERT: A 426 ARG cc_start: 0.6835 (OUTLIER) cc_final: 0.6580 (tpp-160) REVERT: B 559 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8151 (tm-30) outliers start: 23 outliers final: 21 residues processed: 82 average time/residue: 0.9571 time to fit residues: 86.0223 Evaluate side-chains 84 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 62 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 ASP Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 122 THR Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 92 GLN Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 122 THR Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 460 MET Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 556 THR Chi-restraints excluded: chain B residue 637 SER Chi-restraints excluded: chain B residue 645 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.0170 chunk 59 optimal weight: 3.9990 chunk 39 optimal weight: 0.0070 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 31 optimal weight: 0.7980 overall best weight: 0.4436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 141 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.148783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.123288 restraints weight = 55761.504| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 5.85 r_work: 0.3205 rms_B_bonded: 5.68 restraints_weight: 2.0000 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9489 Z= 0.106 Angle : 0.581 11.693 12946 Z= 0.287 Chirality : 0.040 0.229 1538 Planarity : 0.005 0.066 1538 Dihedral : 6.803 52.322 1595 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 2.00 % Allowed : 22.95 % Favored : 75.05 % 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: -1.75 (0.24), residues: 1188 helix: -0.46 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 625 HIS 0.003 0.001 HIS A 541 PHE 0.018 0.001 PHE B 48 TYR 0.007 0.001 TYR A 415 ARG 0.014 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 412) hydrogen bonds : angle 4.32189 ( 1224) SS BOND : bond 0.00037 ( 2) SS BOND : angle 0.77350 ( 4) covalent geometry : bond 0.00244 ( 9487) covalent geometry : angle 0.58096 (12942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2376 Ramachandran restraints generated. 1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.994 Fit side-chains REVERT: A 426 ARG cc_start: 0.6845 (OUTLIER) cc_final: 0.6598 (tpp-160) REVERT: A 514 ARG cc_start: 0.8444 (pmt-80) cc_final: 0.8125 (pmt-80) REVERT: B 559 GLU cc_start: 0.8498 (mt-10) cc_final: 0.8146 (pp20) outliers start: 17 outliers final: 13 residues processed: 80 average time/residue: 1.0552 time to fit residues: 91.9665 Evaluate side-chains 79 residues out of total 942 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 65 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 219 SER Chi-restraints excluded: chain A residue 325 SER Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 426 ARG Chi-restraints excluded: chain A residue 536 THR Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 219 SER Chi-restraints excluded: chain B residue 240 SER Chi-restraints excluded: chain B residue 309 VAL Chi-restraints excluded: chain B residue 327 THR Chi-restraints excluded: chain B residue 536 THR Chi-restraints excluded: chain B residue 637 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 0.0570 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 102 optimal weight: 2.9990 chunk 38 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.148247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.122879 restraints weight = 61774.166| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 5.98 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3534 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3534 r_free = 0.3534 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3534 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.3148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9489 Z= 0.113 Angle : 0.583 11.704 12946 Z= 0.288 Chirality : 0.040 0.221 1538 Planarity : 0.005 0.061 1538 Dihedral : 6.706 48.905 1595 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.79 % Allowed : 22.74 % Favored : 75.47 % 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: -1.63 (0.24), residues: 1188 helix: -0.36 (0.18), residues: 836 sheet: None (None), residues: 0 loop : -2.71 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 625 HIS 0.003 0.001 HIS A 541 PHE 0.017 0.001 PHE B 48 TYR 0.008 0.001 TYR A 415 ARG 0.015 0.000 ARG B 323 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 412) hydrogen bonds : angle 4.30212 ( 1224) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.64090 ( 4) covalent geometry : bond 0.00267 ( 9487) covalent geometry : angle 0.58252 (12942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5888.35 seconds wall clock time: 104 minutes 39.50 seconds (6279.50 seconds total)