Starting phenix.real_space_refine on Mon Mar 11 19:21:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/03_2024/6vxh_21437_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/03_2024/6vxh_21437.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/03_2024/6vxh_21437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/03_2024/6vxh_21437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/03_2024/6vxh_21437_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/03_2024/6vxh_21437_updated.pdb" } resolution = 4.0 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= 0.000 sd= 0.015 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 58 5.16 5 C 5783 2.51 5 N 1457 2.21 5 O 1581 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 96": "NH1" <-> "NH2" Residue "A ARG 160": "NH1" <-> "NH2" Residue "A ARG 184": "NH1" <-> "NH2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 211": "OE1" <-> "OE2" Residue "A ARG 246": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ARG 426": "NH1" <-> "NH2" Residue "A ARG 482": "NH1" <-> "NH2" Residue "A GLU 585": "OE1" <-> "OE2" Residue "B ARG 96": "NH1" <-> "NH2" Residue "B ARG 160": "NH1" <-> "NH2" Residue "B ARG 184": "NH1" <-> "NH2" Residue "B ARG 246": "NH1" <-> "NH2" Residue "B ARG 426": "NH1" <-> "NH2" Residue "B GLU 458": "OE1" <-> "OE2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B GLU 612": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8879 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4393 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 18, 'TRANS': 546} Chain breaks: 3 Chain: "B" Number of atoms: 4393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4393 Classifications: {'peptide': 565} Link IDs: {'PTRANS': 18, 'TRANS': 546} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 65 Unusual residues: {'CLR': 1, 'STI': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.47, per 1000 atoms: 0.62 Number of scatterers: 8879 At special positions: 0 Unit cell: (106.53, 73.6645, 125.796, 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 58 16.00 O 1581 8.00 N 1457 7.00 C 5783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 608 " distance=2.03 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS B 603 " distance=2.15 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 608 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.41 Conformation dependent library (CDL) restraints added in 1.8 seconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2088 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 48 helices and 4 sheets defined 44.2% alpha, 1.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.78 Creating SS restraints... Processing helix chain 'A' and resid 90 through 93 No H-bonds generated for 'chain 'A' and resid 90 through 93' Processing helix chain 'A' and resid 118 through 120 No H-bonds generated for 'chain 'A' and resid 118 through 120' Processing helix chain 'A' and resid 136 through 147 removed outlier: 3.635A pdb=" N SER A 143 " --> pdb=" O ASN A 139 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LEU A 146 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 165 removed outlier: 3.516A pdb=" N ASN A 162 " --> pdb=" O ASN A 158 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N VAL A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 199 removed outlier: 4.039A pdb=" N LYS A 192 " --> pdb=" O GLY A 188 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N ARG A 193 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N THR A 194 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N MET A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N GLU A 199 " --> pdb=" O SER A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 234 removed outlier: 3.662A pdb=" N VAL A 224 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 226 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N LYS A 233 " --> pdb=" O ARG A 230 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLN A 234 " --> pdb=" O MET A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 295 removed outlier: 4.239A pdb=" N PHE A 294 " --> pdb=" O PRO A 290 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N LEU A 295 " --> pdb=" O ALA A 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 290 through 295' Processing helix chain 'A' and resid 329 through 337 removed outlier: 4.505A pdb=" N ILE A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N TYR A 336 " --> pdb=" O LEU A 332 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N VAL A 337 " --> pdb=" O ALA A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 removed outlier: 3.718A pdb=" N LYS A 346 " --> pdb=" O TYR A 342 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N ALA A 347 " --> pdb=" O LYS A 343 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 390 removed outlier: 3.565A pdb=" N LEU A 377 " --> pdb=" O PHE A 373 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ARG A 378 " --> pdb=" O CYS A 374 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 382 " --> pdb=" O ARG A 378 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 383 " --> pdb=" O TRP A 379 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N SER A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 385 " --> pdb=" O SER A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 396 through 398 No H-bonds generated for 'chain 'A' and resid 396 through 398' Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.555A pdb=" N LEU A 405 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU A 407 " --> pdb=" O VAL A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 447 removed outlier: 3.860A pdb=" N VAL A 429 " --> pdb=" O ASN A 425 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU A 433 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N THR A 434 " --> pdb=" O LEU A 430 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N SER A 441 " --> pdb=" O GLN A 437 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N VAL A 442 " --> pdb=" O CYS A 438 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N SER A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ALA A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N VAL A 445 " --> pdb=" O SER A 441 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N GLU A 446 " --> pdb=" O VAL A 442 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N LEU A 447 " --> pdb=" O SER A 443 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 460 removed outlier: 3.826A pdb=" N HIS A 457 " --> pdb=" O LYS A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing helix chain 'A' and resid 484 through 497 removed outlier: 4.414A pdb=" N PHE A 489 " --> pdb=" O PRO A 485 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 492 " --> pdb=" O ILE A 488 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N VAL A 493 " --> pdb=" O PHE A 489 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N PHE A 495 " --> pdb=" O CYS A 491 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N MET A 496 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 526 removed outlier: 3.647A pdb=" N PHE A 511 " --> pdb=" O PHE A 507 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 513 " --> pdb=" O MET A 509 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N TYR A 518 " --> pdb=" O MET A 514 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N MET A 523 " --> pdb=" O SER A 519 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA A 526 " --> pdb=" O SER A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 542 No H-bonds generated for 'chain 'A' and resid 539 through 542' Processing helix chain 'A' and resid 547 through 550 No H-bonds generated for 'chain 'A' and resid 547 through 550' Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 573 through 583 removed outlier: 3.987A pdb=" N GLY A 577 " --> pdb=" O ILE A 573 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 578 " --> pdb=" O PRO A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 616 No H-bonds generated for 'chain 'A' and resid 613 through 616' Processing helix chain 'A' and resid 623 through 649 removed outlier: 3.831A pdb=" N TRP A 627 " --> pdb=" O PRO A 623 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN A 629 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N HIS A 630 " --> pdb=" O LEU A 626 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ALA A 634 " --> pdb=" O HIS A 630 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE A 639 " --> pdb=" O CYS A 635 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LYS A 647 " --> pdb=" O ILE A 643 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU A 649 " --> pdb=" O TYR A 645 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 93 No H-bonds generated for 'chain 'B' and resid 90 through 93' Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 136 through 147 removed outlier: 3.845A pdb=" N LEU B 146 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N ARG B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 157 through 166 removed outlier: 4.343A pdb=" N ARG B 163 " --> pdb=" O GLU B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 removed outlier: 4.424A pdb=" N ARG B 193 " --> pdb=" O GLY B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 234 removed outlier: 3.776A pdb=" N LEU B 225 " --> pdb=" O ALA B 221 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG B 230 " --> pdb=" O LEU B 226 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N MET B 231 " --> pdb=" O LEU B 227 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N GLN B 234 " --> pdb=" O ARG B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 251 No H-bonds generated for 'chain 'B' and resid 248 through 251' Processing helix chain 'B' and resid 277 through 279 No H-bonds generated for 'chain 'B' and resid 277 through 279' Processing helix chain 'B' and resid 290 through 293 No H-bonds generated for 'chain 'B' and resid 290 through 293' Processing helix chain 'B' and resid 296 through 298 No H-bonds generated for 'chain 'B' and resid 296 through 298' Processing helix chain 'B' and resid 329 through 337 removed outlier: 3.550A pdb=" N ALA B 333 " --> pdb=" O ILE B 329 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ILE B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N TYR B 336 " --> pdb=" O LEU B 332 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL B 337 " --> pdb=" O ALA B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 351 removed outlier: 3.831A pdb=" N LYS B 346 " --> pdb=" O TYR B 342 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA B 347 " --> pdb=" O LYS B 343 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLU B 348 " --> pdb=" O GLU B 344 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU B 349 " --> pdb=" O THR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 373 through 389 removed outlier: 3.503A pdb=" N LEU B 377 " --> pdb=" O PHE B 373 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 378 " --> pdb=" O CYS B 374 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER B 381 " --> pdb=" O LEU B 377 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LYS B 382 " --> pdb=" O ARG B 378 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARG B 383 " --> pdb=" O TRP B 379 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 396 through 412 removed outlier: 4.192A pdb=" N ILE B 400 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N VAL B 401 " --> pdb=" O GLN B 398 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL B 404 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU B 405 " --> pdb=" O THR B 402 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N GLY B 406 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N LEU B 407 " --> pdb=" O VAL B 404 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ILE B 409 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ILE B 412 " --> pdb=" O ILE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 444 removed outlier: 4.457A pdb=" N VAL B 429 " --> pdb=" O ASN B 425 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER B 441 " --> pdb=" O GLN B 437 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N VAL B 442 " --> pdb=" O CYS B 438 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N SER B 443 " --> pdb=" O PHE B 439 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA B 444 " --> pdb=" O SER B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 449 through 460 removed outlier: 5.367A pdb=" N LYS B 453 " --> pdb=" O VAL B 450 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ILE B 456 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N HIS B 457 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N TYR B 459 " --> pdb=" O ILE B 456 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE B 460 " --> pdb=" O HIS B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 466 through 474 removed outlier: 3.520A pdb=" N LEU B 471 " --> pdb=" O SER B 467 " (cutoff:3.500A) Processing helix chain 'B' and resid 479 through 482 No H-bonds generated for 'chain 'B' and resid 479 through 482' Processing helix chain 'B' and resid 484 through 497 removed outlier: 4.354A pdb=" N PHE B 489 " --> pdb=" O PRO B 485 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N ILE B 492 " --> pdb=" O ILE B 488 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N VAL B 493 " --> pdb=" O PHE B 489 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N PHE B 495 " --> pdb=" O CYS B 491 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET B 496 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 526 removed outlier: 4.019A pdb=" N PHE B 511 " --> pdb=" O PHE B 507 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N MET B 514 " --> pdb=" O MET B 510 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N TYR B 518 " --> pdb=" O MET B 514 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N SER B 519 " --> pdb=" O MET B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 550 No H-bonds generated for 'chain 'B' and resid 547 through 550' Processing helix chain 'B' and resid 566 through 571 removed outlier: 3.522A pdb=" N GLN B 569 " --> pdb=" O SER B 566 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N TYR B 570 " --> pdb=" O TRP B 567 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N PHE B 571 " --> pdb=" O LEU B 568 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 566 through 571' Processing helix chain 'B' and resid 573 through 583 removed outlier: 3.716A pdb=" N GLY B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 611 through 617 Processing helix chain 'B' and resid 623 through 649 removed outlier: 3.885A pdb=" N TRP B 627 " --> pdb=" O PRO B 623 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N ASN B 629 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N HIS B 630 " --> pdb=" O LEU B 626 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 37 through 40 Processing sheet with id= B, first strand: chain 'A' and resid 206 through 208 removed outlier: 7.047A pdb=" N THR A 237 " --> pdb=" O LEU A 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.566A pdb=" N HIS B 40 " --> pdb=" O ASP B 105 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ASP B 105 " --> pdb=" O HIS B 40 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 206 through 208 removed outlier: 6.977A pdb=" N THR B 237 " --> pdb=" O LEU B 207 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 203 hydrogen bonds defined for protein. 558 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: 1.94 Time building geometry restraints manager: 3.71 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: 1382 1.31 - 1.44: 2451 1.44 - 1.57: 5144 1.57 - 1.70: 0 1.70 - 1.83: 94 Bond restraints: 9071 Sorted by residual: bond pdb=" C22 STI B 701 " pdb=" N21 STI B 701 " ideal model delta sigma weight residual 1.357 1.465 -0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" C9 STI B 701 " pdb=" N13 STI B 701 " ideal model delta sigma weight residual 1.362 1.461 -0.099 2.00e-02 2.50e+03 2.43e+01 bond pdb=" C5 STI B 701 " pdb=" C7 STI B 701 " ideal model delta sigma weight residual 1.475 1.381 0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" C14 STI B 701 " pdb=" N13 STI B 701 " ideal model delta sigma weight residual 1.391 1.460 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" C16 STI B 701 " pdb=" N21 STI B 701 " ideal model delta sigma weight residual 1.401 1.467 -0.066 2.00e-02 2.50e+03 1.08e+01 ... (remaining 9066 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.64: 164 105.64 - 112.73: 4682 112.73 - 119.81: 3244 119.81 - 126.90: 4101 126.90 - 133.99: 95 Bond angle restraints: 12286 Sorted by residual: angle pdb=" C PHE A 266 " pdb=" N HIS A 267 " pdb=" CA HIS A 267 " ideal model delta sigma weight residual 122.36 132.15 -9.79 1.47e+00 4.63e-01 4.44e+01 angle pdb=" C PHE B 266 " pdb=" N HIS B 267 " pdb=" CA HIS B 267 " ideal model delta sigma weight residual 122.36 131.40 -9.04 1.47e+00 4.63e-01 3.78e+01 angle pdb=" C SER A 572 " pdb=" N ILE A 573 " pdb=" CA ILE A 573 " ideal model delta sigma weight residual 120.33 124.81 -4.48 8.00e-01 1.56e+00 3.13e+01 angle pdb=" CA GLU A 211 " pdb=" CB GLU A 211 " pdb=" CG GLU A 211 " ideal model delta sigma weight residual 114.10 124.50 -10.40 2.00e+00 2.50e-01 2.70e+01 angle pdb=" C ASN A 557 " pdb=" N LEU A 558 " pdb=" CA LEU A 558 " ideal model delta sigma weight residual 121.54 130.42 -8.88 1.91e+00 2.74e-01 2.16e+01 ... (remaining 12281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.82: 4943 21.82 - 43.64: 456 43.64 - 65.46: 45 65.46 - 87.27: 10 87.27 - 109.09: 6 Dihedral angle restraints: 5460 sinusoidal: 2208 harmonic: 3252 Sorted by residual: dihedral pdb=" CB CYS A 592 " pdb=" SG CYS A 592 " pdb=" SG CYS A 608 " pdb=" CB CYS A 608 " ideal model delta sinusoidal sigma weight residual 93.00 25.59 67.41 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS B 592 " pdb=" SG CYS B 592 " pdb=" SG CYS B 608 " pdb=" CB CYS B 608 " ideal model delta sinusoidal sigma weight residual 93.00 25.84 67.16 1 1.00e+01 1.00e-02 5.87e+01 dihedral pdb=" CA PHE A 266 " pdb=" C PHE A 266 " pdb=" N HIS A 267 " pdb=" CA HIS A 267 " ideal model delta harmonic sigma weight residual -180.00 -147.56 -32.44 0 5.00e+00 4.00e-02 4.21e+01 ... (remaining 5457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1164 0.069 - 0.137: 223 0.137 - 0.206: 27 0.206 - 0.274: 6 0.274 - 0.343: 4 Chirality restraints: 1424 Sorted by residual: chirality pdb=" C13 CLR A 701 " pdb=" C12 CLR A 701 " pdb=" C14 CLR A 701 " pdb=" C17 CLR A 701 " both_signs ideal model delta sigma weight residual False -2.93 -2.59 -0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CB VAL B 173 " pdb=" CA VAL B 173 " pdb=" CG1 VAL B 173 " pdb=" CG2 VAL B 173 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" CB ILE B 108 " pdb=" CA ILE B 108 " pdb=" CG1 ILE B 108 " pdb=" CG2 ILE B 108 " both_signs ideal model delta sigma weight residual False 2.64 2.33 0.31 2.00e-01 2.50e+01 2.40e+00 ... (remaining 1421 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 484 " -0.047 5.00e-02 4.00e+02 6.96e-02 7.75e+00 pdb=" N PRO A 485 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 485 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 485 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 484 " 0.045 5.00e-02 4.00e+02 6.67e-02 7.13e+00 pdb=" N PRO B 485 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 485 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 485 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THR A 257 " -0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C THR A 257 " 0.044 2.00e-02 2.50e+03 pdb=" O THR A 257 " -0.017 2.00e-02 2.50e+03 pdb=" N LEU A 258 " -0.015 2.00e-02 2.50e+03 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 2172 2.78 - 3.31: 7871 3.31 - 3.84: 13826 3.84 - 4.37: 15557 4.37 - 4.90: 26373 Nonbonded interactions: 65799 Sorted by model distance: nonbonded pdb=" OH TYR A 413 " pdb=" O LEU B 555 " model vdw 2.245 2.440 nonbonded pdb=" O SER B 440 " pdb=" OG SER B 440 " model vdw 2.283 2.440 nonbonded pdb=" NH1 ARG A 575 " pdb=" OG1 THR A 579 " model vdw 2.298 2.520 nonbonded pdb=" O SER A 261 " pdb=" OG SER A 261 " model vdw 2.312 2.440 nonbonded pdb=" O ILE B 335 " pdb=" OG SER B 339 " model vdw 2.313 2.440 ... (remaining 65794 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 35 through 654) selection = (chain 'B' and resid 35 through 654) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.350 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: 0.000 Extract box with map and model: 2.090 Check model and map are aligned: 0.150 Set scattering table: 0.080 Process input model: 27.090 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.006 0.108 9071 Z= 0.408 Angle : 1.067 10.399 12286 Z= 0.589 Chirality : 0.060 0.343 1424 Planarity : 0.006 0.070 1519 Dihedral : 16.225 109.093 3363 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.87 % Favored : 89.95 % Rotamer: Outliers : 0.31 % Allowed : 13.20 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -6.42 (0.16), residues: 1114 helix: -4.61 (0.09), residues: 526 sheet: -4.53 (0.73), residues: 24 loop : -3.94 (0.20), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 564 HIS 0.008 0.001 HIS A 267 PHE 0.026 0.002 PHE A 489 TYR 0.014 0.002 TYR A 342 ARG 0.006 0.001 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 195 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 126 GLN cc_start: 0.8114 (tm-30) cc_final: 0.7794 (tm-30) REVERT: A 127 ASP cc_start: 0.8178 (m-30) cc_final: 0.7975 (m-30) REVERT: A 190 GLU cc_start: 0.7686 (mt-10) cc_final: 0.7438 (mp0) REVERT: A 523 MET cc_start: 0.9087 (ttt) cc_final: 0.8830 (ttm) REVERT: A 567 TRP cc_start: 0.8948 (p-90) cc_final: 0.8364 (p-90) REVERT: A 643 ILE cc_start: 0.9335 (pt) cc_final: 0.8922 (mt) REVERT: B 242 ILE cc_start: 0.9181 (tp) cc_final: 0.8970 (tp) REVERT: B 252 LEU cc_start: 0.9174 (tp) cc_final: 0.8967 (tp) REVERT: B 253 PHE cc_start: 0.8610 (m-10) cc_final: 0.8407 (m-80) REVERT: B 296 ASP cc_start: 0.7141 (t0) cc_final: 0.6752 (t0) REVERT: B 413 TYR cc_start: 0.8504 (m-80) cc_final: 0.8197 (m-80) REVERT: B 492 ILE cc_start: 0.8965 (tp) cc_final: 0.8753 (mm) REVERT: B 541 MET cc_start: 0.8505 (tmm) cc_final: 0.8235 (tmm) REVERT: B 548 MET cc_start: 0.8164 (mtt) cc_final: 0.7777 (mtt) REVERT: B 549 MET cc_start: 0.8392 (ttp) cc_final: 0.8182 (tmm) REVERT: B 573 ILE cc_start: 0.9390 (mt) cc_final: 0.9148 (mt) REVERT: B 643 ILE cc_start: 0.9502 (pt) cc_final: 0.9211 (tt) outliers start: 3 outliers final: 2 residues processed: 196 average time/residue: 0.1983 time to fit residues: 54.0351 Evaluate side-chains 145 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain B residue 63 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 0.0770 chunk 28 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 overall best weight: 1.5744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 ASN A 109 ASN A 120 ASN ** A 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 418 ASN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 76 ASN B 109 ASN B 289 ASN B 393 GLN B 398 GLN B 418 ASN B 601 ASN B 630 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9071 Z= 0.208 Angle : 0.689 8.817 12286 Z= 0.348 Chirality : 0.043 0.175 1424 Planarity : 0.004 0.053 1519 Dihedral : 8.383 71.503 1353 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 9.16 % Favored : 90.75 % Rotamer: Outliers : 2.60 % Allowed : 21.31 % Favored : 76.09 % 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: -4.90 (0.20), residues: 1114 helix: -2.99 (0.17), residues: 494 sheet: -4.48 (0.72), residues: 24 loop : -3.52 (0.21), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.008 0.001 HIS A 243 PHE 0.013 0.001 PHE B 591 TYR 0.013 0.001 TYR B 342 ARG 0.004 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 153 time to evaluate : 1.365 Fit side-chains REVERT: A 106 VAL cc_start: 0.9033 (OUTLIER) cc_final: 0.8800 (m) REVERT: A 107 LEU cc_start: 0.8870 (mm) cc_final: 0.8654 (tp) REVERT: A 124 VAL cc_start: 0.9226 (OUTLIER) cc_final: 0.8909 (m) REVERT: A 283 HIS cc_start: 0.6069 (m-70) cc_final: 0.5713 (m-70) REVERT: A 523 MET cc_start: 0.9157 (ttt) cc_final: 0.8844 (ttp) REVERT: A 567 TRP cc_start: 0.8884 (p-90) cc_final: 0.8328 (p-90) REVERT: A 635 CYS cc_start: 0.8665 (m) cc_final: 0.8447 (t) REVERT: B 131 MET cc_start: 0.8574 (mmm) cc_final: 0.8210 (mmm) REVERT: B 199 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7541 (mm-30) REVERT: B 252 LEU cc_start: 0.9200 (tp) cc_final: 0.8959 (tp) REVERT: B 253 PHE cc_start: 0.8615 (m-10) cc_final: 0.8373 (m-80) REVERT: B 296 ASP cc_start: 0.7148 (t0) cc_final: 0.6920 (t0) REVERT: B 385 PHE cc_start: 0.8468 (t80) cc_final: 0.8247 (t80) REVERT: B 413 TYR cc_start: 0.8366 (m-80) cc_final: 0.8116 (m-80) REVERT: B 481 MET cc_start: 0.8477 (tpp) cc_final: 0.7977 (ttt) REVERT: B 492 ILE cc_start: 0.8947 (tp) cc_final: 0.8631 (tp) REVERT: B 514 MET cc_start: 0.8786 (tmm) cc_final: 0.8291 (tmm) REVERT: B 541 MET cc_start: 0.8629 (tmm) cc_final: 0.8054 (tmm) outliers start: 25 outliers final: 11 residues processed: 172 average time/residue: 0.1658 time to fit residues: 43.0805 Evaluate side-chains 138 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 124 VAL Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 592 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 56 optimal weight: 10.0000 chunk 31 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 629 ASN B 40 HIS B 283 HIS B 375 HIS B 424 GLN B 629 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9071 Z= 0.414 Angle : 0.773 9.000 12286 Z= 0.394 Chirality : 0.048 0.191 1424 Planarity : 0.005 0.048 1519 Dihedral : 7.882 88.779 1353 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.84 % Favored : 87.07 % Rotamer: Outliers : 5.61 % Allowed : 22.97 % Favored : 71.41 % 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: -4.24 (0.22), residues: 1114 helix: -2.26 (0.20), residues: 504 sheet: -4.96 (0.47), residues: 36 loop : -3.25 (0.24), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 379 HIS 0.007 0.001 HIS B 630 PHE 0.019 0.002 PHE A 489 TYR 0.024 0.002 TYR A 463 ARG 0.005 0.001 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 128 time to evaluate : 1.007 Fit side-chains revert: symmetry clash REVERT: A 106 VAL cc_start: 0.9121 (OUTLIER) cc_final: 0.8819 (p) REVERT: A 107 LEU cc_start: 0.8931 (mm) cc_final: 0.8646 (tp) REVERT: A 228 LEU cc_start: 0.9597 (OUTLIER) cc_final: 0.9367 (mm) REVERT: A 283 HIS cc_start: 0.5763 (m-70) cc_final: 0.5467 (m-70) REVERT: A 458 GLU cc_start: 0.8649 (mm-30) cc_final: 0.8379 (tp30) REVERT: A 483 MET cc_start: 0.8625 (tmm) cc_final: 0.7661 (tmm) REVERT: A 514 MET cc_start: 0.8012 (tmm) cc_final: 0.7642 (tmm) REVERT: A 523 MET cc_start: 0.9207 (ttt) cc_final: 0.8620 (ttp) REVERT: A 567 TRP cc_start: 0.9021 (p-90) cc_final: 0.8448 (p-90) REVERT: B 90 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8322 (tt) REVERT: B 253 PHE cc_start: 0.8631 (m-10) cc_final: 0.8237 (m-80) REVERT: B 296 ASP cc_start: 0.7283 (t0) cc_final: 0.7068 (t0) REVERT: B 413 TYR cc_start: 0.8449 (m-80) cc_final: 0.8187 (m-80) REVERT: B 492 ILE cc_start: 0.9038 (tp) cc_final: 0.8729 (tp) REVERT: B 509 MET cc_start: 0.9110 (ttt) cc_final: 0.8719 (ttt) REVERT: B 541 MET cc_start: 0.8507 (tmm) cc_final: 0.7825 (tmm) REVERT: B 548 MET cc_start: 0.7988 (mtt) cc_final: 0.7643 (mtm) outliers start: 54 outliers final: 36 residues processed: 170 average time/residue: 0.1433 time to fit residues: 38.3055 Evaluate side-chains 157 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 118 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 214 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 38 SER Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 603 CYS Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 102 optimal weight: 0.3980 chunk 108 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN B 375 HIS B 557 ASN B 583 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.2503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9071 Z= 0.172 Angle : 0.616 9.363 12286 Z= 0.309 Chirality : 0.042 0.176 1424 Planarity : 0.003 0.037 1519 Dihedral : 7.310 77.240 1353 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer: Outliers : 4.78 % Allowed : 25.88 % Favored : 69.33 % 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: -3.65 (0.23), residues: 1114 helix: -1.66 (0.22), residues: 508 sheet: -3.25 (0.65), residues: 44 loop : -3.15 (0.24), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS B 267 PHE 0.013 0.001 PHE B 506 TYR 0.015 0.001 TYR A 276 ARG 0.002 0.000 ARG B 236 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 138 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8332 (mmt) cc_final: 0.8121 (mmt) REVERT: A 107 LEU cc_start: 0.8846 (mm) cc_final: 0.8627 (tp) REVERT: A 131 MET cc_start: 0.8483 (mmt) cc_final: 0.7977 (mtp) REVERT: A 190 GLU cc_start: 0.7703 (OUTLIER) cc_final: 0.7415 (mp0) REVERT: A 283 HIS cc_start: 0.5438 (m-70) cc_final: 0.5222 (m-70) REVERT: A 458 GLU cc_start: 0.8317 (mm-30) cc_final: 0.7768 (mm-30) REVERT: A 483 MET cc_start: 0.8636 (tmm) cc_final: 0.7484 (tmm) REVERT: A 567 TRP cc_start: 0.8866 (p-90) cc_final: 0.8342 (p-90) REVERT: B 253 PHE cc_start: 0.8549 (m-10) cc_final: 0.8257 (m-80) REVERT: B 413 TYR cc_start: 0.8444 (m-80) cc_final: 0.8210 (m-80) REVERT: B 492 ILE cc_start: 0.8965 (tp) cc_final: 0.8632 (tp) REVERT: B 496 MET cc_start: 0.8614 (tpp) cc_final: 0.8400 (tpp) REVERT: B 509 MET cc_start: 0.9056 (ttt) cc_final: 0.8652 (ttt) REVERT: B 514 MET cc_start: 0.9034 (tmm) cc_final: 0.8653 (tmm) REVERT: B 515 MET cc_start: 0.8835 (tpp) cc_final: 0.8302 (tpp) REVERT: B 541 MET cc_start: 0.8382 (tmm) cc_final: 0.7872 (tmm) REVERT: B 548 MET cc_start: 0.7935 (mtt) cc_final: 0.7489 (mtm) REVERT: B 568 LEU cc_start: 0.9255 (OUTLIER) cc_final: 0.9024 (tt) REVERT: B 573 ILE cc_start: 0.9326 (mt) cc_final: 0.8967 (mt) outliers start: 46 outliers final: 22 residues processed: 172 average time/residue: 0.1431 time to fit residues: 38.5455 Evaluate side-chains 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 126 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 190 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 568 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 92 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 97 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 6.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9071 Z= 0.254 Angle : 0.650 9.504 12286 Z= 0.328 Chirality : 0.044 0.201 1424 Planarity : 0.004 0.042 1519 Dihedral : 7.217 82.605 1353 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.03 % Favored : 87.97 % Rotamer: Outliers : 5.82 % Allowed : 25.57 % Favored : 68.61 % 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: -3.34 (0.24), residues: 1114 helix: -1.37 (0.23), residues: 508 sheet: -3.20 (0.66), residues: 44 loop : -3.02 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.004 0.001 HIS A 630 PHE 0.012 0.001 PHE A 506 TYR 0.016 0.002 TYR B 336 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 125 time to evaluate : 1.195 Fit side-chains revert: symmetry clash REVERT: A 148 LEU cc_start: 0.8566 (OUTLIER) cc_final: 0.7961 (pp) REVERT: A 483 MET cc_start: 0.8751 (tmm) cc_final: 0.7554 (tmm) REVERT: A 523 MET cc_start: 0.9120 (ttt) cc_final: 0.8485 (ttp) REVERT: A 567 TRP cc_start: 0.8954 (p-90) cc_final: 0.8401 (p-90) REVERT: A 645 TYR cc_start: 0.8900 (t80) cc_final: 0.8651 (t80) REVERT: B 199 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7507 (mm-30) REVERT: B 253 PHE cc_start: 0.8517 (m-10) cc_final: 0.8127 (m-80) REVERT: B 492 ILE cc_start: 0.8998 (tp) cc_final: 0.8699 (tp) REVERT: B 509 MET cc_start: 0.9105 (ttt) cc_final: 0.8682 (ttt) REVERT: B 514 MET cc_start: 0.9076 (tmm) cc_final: 0.8659 (tmm) REVERT: B 523 MET cc_start: 0.8785 (OUTLIER) cc_final: 0.7749 (ttp) REVERT: B 540 LEU cc_start: 0.9178 (tt) cc_final: 0.8952 (tp) REVERT: B 541 MET cc_start: 0.8410 (tmm) cc_final: 0.7895 (tmm) REVERT: B 548 MET cc_start: 0.8003 (mtt) cc_final: 0.7677 (mtm) REVERT: B 568 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8956 (tt) REVERT: B 573 ILE cc_start: 0.9320 (mt) cc_final: 0.8913 (mt) outliers start: 56 outliers final: 41 residues processed: 169 average time/residue: 0.1448 time to fit residues: 38.1722 Evaluate side-chains 165 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 121 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 135 THR Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 206 ILE Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 108 optimal weight: 6.9990 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.005 0.049 9071 Z= 0.350 Angle : 0.720 9.650 12286 Z= 0.361 Chirality : 0.046 0.191 1424 Planarity : 0.004 0.036 1519 Dihedral : 7.403 89.432 1353 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.48 % Favored : 87.52 % Rotamer: Outliers : 6.96 % Allowed : 25.57 % Favored : 67.46 % 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: -3.28 (0.24), residues: 1114 helix: -1.23 (0.23), residues: 496 sheet: -3.57 (0.56), residues: 56 loop : -2.98 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.006 0.001 HIS A 630 PHE 0.014 0.002 PHE A 489 TYR 0.019 0.002 TYR B 336 ARG 0.004 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 125 time to evaluate : 1.071 Fit side-chains REVERT: A 131 MET cc_start: 0.8529 (mmt) cc_final: 0.8065 (mtp) REVERT: A 148 LEU cc_start: 0.8556 (OUTLIER) cc_final: 0.7943 (pp) REVERT: A 458 GLU cc_start: 0.8632 (tp30) cc_final: 0.8218 (tp30) REVERT: A 483 MET cc_start: 0.8839 (tmm) cc_final: 0.7578 (tmm) REVERT: A 523 MET cc_start: 0.9069 (ttt) cc_final: 0.8439 (ttp) REVERT: A 541 MET cc_start: 0.8103 (tmm) cc_final: 0.7485 (tmm) REVERT: A 567 TRP cc_start: 0.9019 (p-90) cc_final: 0.8444 (p-90) REVERT: B 90 LEU cc_start: 0.8714 (OUTLIER) cc_final: 0.8457 (tt) REVERT: B 199 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 253 PHE cc_start: 0.8537 (m-10) cc_final: 0.8065 (m-80) REVERT: B 265 MET cc_start: 0.5782 (mmm) cc_final: 0.5529 (tmm) REVERT: B 413 TYR cc_start: 0.8579 (m-80) cc_final: 0.8367 (m-10) REVERT: B 492 ILE cc_start: 0.9025 (tp) cc_final: 0.8721 (tp) REVERT: B 523 MET cc_start: 0.8799 (OUTLIER) cc_final: 0.7802 (ttp) REVERT: B 541 MET cc_start: 0.8421 (tmm) cc_final: 0.8048 (tmm) REVERT: B 548 MET cc_start: 0.8004 (mtt) cc_final: 0.7657 (mtm) REVERT: B 568 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9062 (tt) REVERT: B 573 ILE cc_start: 0.9262 (mt) cc_final: 0.8912 (mt) outliers start: 67 outliers final: 52 residues processed: 177 average time/residue: 0.1438 time to fit residues: 39.4778 Evaluate side-chains 176 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 120 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 403 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 79 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 chunk 107 optimal weight: 10.0000 chunk 67 optimal weight: 4.9990 chunk 65 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9071 Z= 0.299 Angle : 0.690 9.889 12286 Z= 0.345 Chirality : 0.044 0.197 1424 Planarity : 0.004 0.036 1519 Dihedral : 7.254 86.956 1353 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 6.13 % Allowed : 27.65 % Favored : 66.22 % 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: -3.27 (0.24), residues: 1114 helix: -1.15 (0.23), residues: 516 sheet: -4.81 (0.47), residues: 36 loop : -3.06 (0.25), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS B 630 PHE 0.010 0.002 PHE A 208 TYR 0.021 0.002 TYR A 645 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 123 time to evaluate : 1.072 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.8548 (mmt) cc_final: 0.8118 (mtp) REVERT: A 148 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.7936 (pp) REVERT: A 458 GLU cc_start: 0.8621 (tp30) cc_final: 0.8193 (tp30) REVERT: A 483 MET cc_start: 0.8890 (tmm) cc_final: 0.7567 (tmm) REVERT: A 523 MET cc_start: 0.9000 (ttt) cc_final: 0.8345 (ttp) REVERT: A 541 MET cc_start: 0.8089 (tmm) cc_final: 0.7432 (tmm) REVERT: A 567 TRP cc_start: 0.9005 (p-90) cc_final: 0.8443 (p-90) REVERT: B 199 GLU cc_start: 0.7969 (mm-30) cc_final: 0.7340 (mm-30) REVERT: B 253 PHE cc_start: 0.8464 (m-10) cc_final: 0.8008 (m-80) REVERT: B 265 MET cc_start: 0.5871 (mmm) cc_final: 0.5626 (tmm) REVERT: B 413 TYR cc_start: 0.8573 (m-80) cc_final: 0.8327 (m-10) REVERT: B 492 ILE cc_start: 0.9007 (tp) cc_final: 0.8702 (tp) REVERT: B 523 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.7736 (ttp) REVERT: B 541 MET cc_start: 0.8446 (tmm) cc_final: 0.8089 (tmm) REVERT: B 548 MET cc_start: 0.8089 (mtt) cc_final: 0.7752 (mtm) REVERT: B 568 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.9037 (tt) REVERT: B 573 ILE cc_start: 0.9267 (mt) cc_final: 0.8897 (mt) outliers start: 59 outliers final: 52 residues processed: 169 average time/residue: 0.1470 time to fit residues: 38.9922 Evaluate side-chains 172 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 117 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 154 ASN Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 476 SER Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 8.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 98 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9071 Z= 0.272 Angle : 0.675 9.935 12286 Z= 0.338 Chirality : 0.044 0.226 1424 Planarity : 0.004 0.036 1519 Dihedral : 7.159 86.609 1353 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.30 % Favored : 87.70 % Rotamer: Outliers : 6.96 % Allowed : 27.86 % Favored : 65.18 % 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: -3.16 (0.24), residues: 1114 helix: -1.09 (0.23), residues: 526 sheet: -4.79 (0.48), residues: 36 loop : -2.99 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 379 HIS 0.004 0.001 HIS B 630 PHE 0.011 0.002 PHE A 506 TYR 0.027 0.002 TYR A 645 ARG 0.003 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 125 time to evaluate : 1.029 Fit side-chains revert: symmetry clash REVERT: A 131 MET cc_start: 0.8536 (mmt) cc_final: 0.8113 (mtp) REVERT: A 148 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8121 (pp) REVERT: A 458 GLU cc_start: 0.8581 (tp30) cc_final: 0.8118 (tp30) REVERT: A 483 MET cc_start: 0.8892 (tmm) cc_final: 0.7532 (tmm) REVERT: A 523 MET cc_start: 0.8985 (ttt) cc_final: 0.8333 (ttp) REVERT: A 541 MET cc_start: 0.8155 (tmm) cc_final: 0.7663 (tmm) REVERT: A 567 TRP cc_start: 0.9002 (p-90) cc_final: 0.8437 (p-90) REVERT: B 199 GLU cc_start: 0.7967 (mm-30) cc_final: 0.7224 (mm-30) REVERT: B 253 PHE cc_start: 0.8458 (m-10) cc_final: 0.8000 (m-80) REVERT: B 265 MET cc_start: 0.5904 (mmm) cc_final: 0.5564 (tmm) REVERT: B 413 TYR cc_start: 0.8560 (m-80) cc_final: 0.8336 (m-10) REVERT: B 492 ILE cc_start: 0.8970 (tp) cc_final: 0.8653 (tp) REVERT: B 496 MET cc_start: 0.8531 (tpp) cc_final: 0.8316 (tpp) REVERT: B 523 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.7710 (ttp) REVERT: B 541 MET cc_start: 0.8401 (tmm) cc_final: 0.8117 (tmm) REVERT: B 548 MET cc_start: 0.8092 (mtt) cc_final: 0.7793 (mtm) REVERT: B 568 LEU cc_start: 0.9278 (OUTLIER) cc_final: 0.9032 (tt) outliers start: 67 outliers final: 53 residues processed: 177 average time/residue: 0.1400 time to fit residues: 38.7652 Evaluate side-chains 179 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 123 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 295 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 642 THR Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 642 THR Chi-restraints excluded: chain B residue 648 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 30 optimal weight: 5.9990 chunk 90 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 106 optimal weight: 0.0970 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 557 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.3284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9071 Z= 0.237 Angle : 0.672 10.211 12286 Z= 0.331 Chirality : 0.043 0.212 1424 Planarity : 0.003 0.037 1519 Dihedral : 7.032 85.020 1353 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 6.24 % Allowed : 28.48 % Favored : 65.28 % 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: -2.96 (0.25), residues: 1114 helix: -0.93 (0.23), residues: 524 sheet: -4.52 (0.66), residues: 24 loop : -2.95 (0.25), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.004 0.001 HIS B 267 PHE 0.016 0.001 PHE B 506 TYR 0.026 0.001 TYR A 645 ARG 0.002 0.000 ARG A 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 126 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9416 (pt) cc_final: 0.9054 (mm) REVERT: A 131 MET cc_start: 0.8553 (mmt) cc_final: 0.8039 (mtp) REVERT: A 148 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8040 (pp) REVERT: A 458 GLU cc_start: 0.8596 (tp30) cc_final: 0.8163 (tp30) REVERT: A 483 MET cc_start: 0.8870 (tmm) cc_final: 0.7482 (tmm) REVERT: A 523 MET cc_start: 0.8959 (ttt) cc_final: 0.8260 (ttp) REVERT: A 527 ILE cc_start: 0.9354 (pt) cc_final: 0.8916 (mt) REVERT: A 541 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7716 (tmm) REVERT: A 567 TRP cc_start: 0.8984 (p-90) cc_final: 0.8425 (p-90) REVERT: B 131 MET cc_start: 0.8505 (mmm) cc_final: 0.8006 (mmm) REVERT: B 199 GLU cc_start: 0.7857 (mm-30) cc_final: 0.7089 (mm-30) REVERT: B 253 PHE cc_start: 0.8407 (m-10) cc_final: 0.7962 (m-80) REVERT: B 265 MET cc_start: 0.5900 (mmm) cc_final: 0.5609 (tmm) REVERT: B 413 TYR cc_start: 0.8550 (m-80) cc_final: 0.8291 (m-10) REVERT: B 481 MET cc_start: 0.8270 (tpp) cc_final: 0.7809 (ttt) REVERT: B 492 ILE cc_start: 0.8940 (tp) cc_final: 0.8625 (tp) REVERT: B 496 MET cc_start: 0.8566 (tpp) cc_final: 0.8359 (tpp) REVERT: B 523 MET cc_start: 0.8783 (OUTLIER) cc_final: 0.7706 (ttp) REVERT: B 541 MET cc_start: 0.8392 (tmm) cc_final: 0.8103 (tmm) REVERT: B 548 MET cc_start: 0.8011 (mtt) cc_final: 0.7643 (ttm) REVERT: B 568 LEU cc_start: 0.9265 (OUTLIER) cc_final: 0.9021 (tt) outliers start: 60 outliers final: 54 residues processed: 173 average time/residue: 0.1461 time to fit residues: 39.2956 Evaluate side-chains 180 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 122 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 108 ILE Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 199 GLU Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain A residue 643 ILE Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 559 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 596 ASN Chi-restraints excluded: chain B residue 620 ASP Chi-restraints excluded: chain B residue 639 ILE Chi-restraints excluded: chain B residue 648 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 111 optimal weight: 0.8980 chunk 102 optimal weight: 0.3980 chunk 88 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 54 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9071 Z= 0.165 Angle : 0.636 10.501 12286 Z= 0.309 Chirality : 0.042 0.220 1424 Planarity : 0.003 0.038 1519 Dihedral : 6.728 78.555 1353 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 4.78 % Allowed : 29.94 % Favored : 65.28 % 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: -2.66 (0.25), residues: 1114 helix: -0.64 (0.24), residues: 516 sheet: -4.21 (0.71), residues: 24 loop : -2.83 (0.25), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 379 HIS 0.006 0.001 HIS B 267 PHE 0.017 0.001 PHE B 506 TYR 0.031 0.001 TYR A 645 ARG 0.002 0.000 ARG A 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 137 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 ILE cc_start: 0.9436 (pt) cc_final: 0.9101 (mm) REVERT: A 148 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.7958 (pp) REVERT: A 458 GLU cc_start: 0.8569 (tp30) cc_final: 0.8103 (tp30) REVERT: A 483 MET cc_start: 0.8773 (tmm) cc_final: 0.7448 (tmm) REVERT: A 541 MET cc_start: 0.8159 (OUTLIER) cc_final: 0.7590 (tmm) REVERT: B 131 MET cc_start: 0.8477 (mmm) cc_final: 0.7899 (mmm) REVERT: B 199 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7037 (mm-30) REVERT: B 253 PHE cc_start: 0.8391 (m-10) cc_final: 0.7912 (m-80) REVERT: B 481 MET cc_start: 0.8255 (tpp) cc_final: 0.7702 (ttt) REVERT: B 492 ILE cc_start: 0.8852 (tp) cc_final: 0.8528 (tp) REVERT: B 509 MET cc_start: 0.9207 (ttm) cc_final: 0.8928 (ttm) REVERT: B 523 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.7706 (ttp) REVERT: B 548 MET cc_start: 0.7838 (mtt) cc_final: 0.7531 (mtm) REVERT: B 568 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8929 (tt) REVERT: B 636 MET cc_start: 0.9135 (tpp) cc_final: 0.8816 (tpp) outliers start: 46 outliers final: 37 residues processed: 170 average time/residue: 0.1571 time to fit residues: 40.5771 Evaluate side-chains 167 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 126 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 ILE Chi-restraints excluded: chain A residue 89 LEU Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 150 THR Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 203 ASP Chi-restraints excluded: chain A residue 226 LEU Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 492 ILE Chi-restraints excluded: chain A residue 532 SER Chi-restraints excluded: chain A residue 541 MET Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain A residue 600 ASN Chi-restraints excluded: chain A residue 608 CYS Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 635 CYS Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 68 ASN Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 108 ILE Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 206 ILE Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 435 THR Chi-restraints excluded: chain B residue 450 VAL Chi-restraints excluded: chain B residue 523 MET Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 592 CYS Chi-restraints excluded: chain B residue 620 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 8.9990 chunk 81 optimal weight: 6.9990 chunk 13 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 11 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 5 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.087991 restraints weight = 17448.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090742 restraints weight = 10124.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092618 restraints weight = 7009.405| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 9071 Z= 0.397 Angle : 0.773 10.899 12286 Z= 0.387 Chirality : 0.048 0.226 1424 Planarity : 0.004 0.035 1519 Dihedral : 7.071 84.821 1353 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.21 % Favored : 87.79 % Rotamer: Outliers : 5.82 % Allowed : 29.42 % Favored : 64.76 % 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: -2.96 (0.25), residues: 1114 helix: -0.92 (0.23), residues: 520 sheet: -4.76 (0.54), residues: 36 loop : -2.87 (0.26), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 379 HIS 0.006 0.001 HIS A 630 PHE 0.018 0.002 PHE A 489 TYR 0.021 0.002 TYR A 645 ARG 0.003 0.000 ARG B 482 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1726.94 seconds wall clock time: 32 minutes 21.24 seconds (1941.24 seconds total)