Starting phenix.real_space_refine (version: dev) on Thu May 12 23:39:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/05_2022/6vxh_21437_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/05_2022/6vxh_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_21437/05_2022/6vxh_21437.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/05_2022/6vxh_21437.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/05_2022/6vxh_21437_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6vxh_21437/05_2022/6vxh_21437_updated.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/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: {'STI': 1, 'CLR': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.64, per 1000 atoms: 0.64 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: 3.31 Conformation dependent library (CDL) restraints added in 1.4 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: 0.94 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: 2.06 Time building geometry restraints manager: 3.65 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 - 19.20: 4735 19.20 - 38.40: 514 38.40 - 57.60: 80 57.60 - 76.80: 11 76.80 - 96.00: 4 Dihedral angle restraints: 5344 sinusoidal: 2092 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 5341 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 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. 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: 0.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.380 Check model and map are aligned: 0.130 Convert atoms to be neutral: 0.070 Process input model: 25.490 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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: 31.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 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 : 15.586 95.996 3247 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.18 % Allowed : 9.87 % Favored : 89.95 % Rotamer Outliers : 0.31 % 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 *********************** 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 : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 196 average time/residue: 0.1978 time to fit residues: 54.0794 Evaluate side-chains 138 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 136 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0836 time to fit residues: 1.7992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 7.9990 chunk 65 optimal weight: 6.9990 chunk 101 optimal weight: 0.7980 overall best weight: 2.5184 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.070 9071 Z= 0.272 Angle : 0.733 9.321 12286 Z= 0.375 Chirality : 0.045 0.175 1424 Planarity : 0.006 0.101 1519 Dihedral : 7.702 76.550 1233 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 10.32 % Favored : 89.59 % Rotamer Outliers : 3.33 % 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: -4.85 (0.20), residues: 1114 helix: -2.95 (0.18), residues: 500 sheet: -4.58 (0.68), residues: 24 loop : -3.48 (0.22), residues: 590 *********************** 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 172 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 140 time to evaluate : 1.237 Fit side-chains outliers start: 32 outliers final: 16 residues processed: 163 average time/residue: 0.1614 time to fit residues: 39.7375 Evaluate side-chains 128 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 112 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0830 time to fit residues: 3.9701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 84 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 110 optimal weight: 0.9980 chunk 90 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 overall best weight: 1.9782 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 ASN ** A 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 629 ASN B 40 HIS B 283 HIS B 557 ASN B 583 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 9071 Z= 0.227 Angle : 0.659 9.274 12286 Z= 0.332 Chirality : 0.043 0.188 1424 Planarity : 0.005 0.058 1519 Dihedral : 7.435 77.675 1233 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.05 % Favored : 89.95 % Rotamer Outliers : 3.22 % 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: -4.16 (0.22), residues: 1114 helix: -2.18 (0.21), residues: 506 sheet: -4.54 (0.70), residues: 24 loop : -3.31 (0.23), residues: 584 *********************** 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 167 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 16 residues processed: 159 average time/residue: 0.1470 time to fit residues: 36.0082 Evaluate side-chains 137 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0803 time to fit residues: 3.8814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 76 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 53 optimal weight: 8.9990 chunk 96 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 569 GLN A 617 GLN B 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.098 9071 Z= 0.186 Angle : 0.656 12.333 12286 Z= 0.326 Chirality : 0.041 0.188 1424 Planarity : 0.005 0.080 1519 Dihedral : 7.208 75.705 1233 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % Rotamer Outliers : 2.60 % 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: -1.63 (0.22), residues: 506 sheet: -4.30 (0.75), residues: 24 loop : -3.16 (0.24), residues: 584 *********************** 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 163 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 0.988 Fit side-chains revert: symmetry clash outliers start: 25 outliers final: 16 residues processed: 156 average time/residue: 0.1543 time to fit residues: 36.9145 Evaluate side-chains 142 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 126 time to evaluate : 1.035 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.0829 time to fit residues: 4.0175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 61 optimal weight: 0.0370 chunk 1 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 44 optimal weight: 0.0270 chunk 92 optimal weight: 3.9990 chunk 74 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 0.0980 chunk 97 optimal weight: 0.0980 chunk 27 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 0.1916 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 583 HIS B 283 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 9071 Z= 0.153 Angle : 0.618 11.657 12286 Z= 0.306 Chirality : 0.040 0.193 1424 Planarity : 0.004 0.088 1519 Dihedral : 6.897 69.149 1233 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer Outliers : 1.77 % 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: -3.24 (0.24), residues: 1114 helix: -1.21 (0.23), residues: 506 sheet: -3.97 (0.86), residues: 24 loop : -3.04 (0.24), residues: 584 *********************** 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 169 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 152 time to evaluate : 1.141 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 3 residues processed: 163 average time/residue: 0.1630 time to fit residues: 39.8862 Evaluate side-chains 128 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0893 time to fit residues: 1.8970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 108 optimal weight: 0.0010 chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 104 optimal weight: 0.9980 overall best weight: 2.1992 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN B 424 GLN B 629 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.178 9071 Z= 0.250 Angle : 0.692 12.344 12286 Z= 0.347 Chirality : 0.043 0.199 1424 Planarity : 0.004 0.075 1519 Dihedral : 6.881 77.783 1233 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.96 % Favored : 90.04 % Rotamer Outliers : 2.39 % 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: -3.08 (0.24), residues: 1114 helix: -1.08 (0.24), residues: 502 sheet: -4.27 (0.77), residues: 24 loop : -2.91 (0.24), residues: 588 *********************** 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 150 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 127 time to evaluate : 1.040 Fit side-chains outliers start: 23 outliers final: 12 residues processed: 139 average time/residue: 0.1568 time to fit residues: 33.0996 Evaluate side-chains 133 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 1.074 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0798 time to fit residues: 3.1758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 79 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 60 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 49 optimal weight: 0.9980 chunk 66 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- 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 120 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 617 GLN B 299 ASN B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.055 9071 Z= 0.431 Angle : 0.816 10.039 12286 Z= 0.408 Chirality : 0.048 0.204 1424 Planarity : 0.006 0.090 1519 Dihedral : 7.365 85.341 1233 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.39 % Favored : 87.61 % Rotamer Outliers : 3.43 % 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: -3.37 (0.24), residues: 1114 helix: -1.37 (0.22), residues: 522 sheet: -4.75 (0.51), residues: 36 loop : -2.98 (0.25), residues: 556 *********************** 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 155 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 122 time to evaluate : 1.055 Fit side-chains revert: symmetry clash outliers start: 33 outliers final: 19 residues processed: 139 average time/residue: 0.1542 time to fit residues: 33.1330 Evaluate side-chains 132 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 1.089 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.0884 time to fit residues: 4.4516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 68 optimal weight: 0.0770 chunk 73 optimal weight: 7.9990 chunk 53 optimal weight: 0.7980 chunk 10 optimal weight: 10.0000 chunk 84 optimal weight: 9.9990 chunk 98 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- 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 120 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** A 557 ASN B 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.069 9071 Z= 0.231 Angle : 0.705 12.176 12286 Z= 0.348 Chirality : 0.043 0.209 1424 Planarity : 0.006 0.148 1519 Dihedral : 7.108 82.202 1233 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer Outliers : 1.14 % 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: -3.06 (0.25), residues: 1114 helix: -1.11 (0.23), residues: 526 sheet: -4.68 (0.64), residues: 24 loop : -2.89 (0.25), residues: 564 *********************** 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 142 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 131 time to evaluate : 0.977 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 136 average time/residue: 0.1503 time to fit residues: 31.5972 Evaluate side-chains 129 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 121 time to evaluate : 0.992 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0840 time to fit residues: 2.6462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 66 optimal weight: 0.0770 chunk 106 optimal weight: 10.0000 overall best weight: 1.3944 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 HIS ** A 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 557 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 9071 Z= 0.210 Angle : 0.687 11.905 12286 Z= 0.336 Chirality : 0.043 0.222 1424 Planarity : 0.005 0.120 1519 Dihedral : 6.942 78.746 1233 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.87 % Favored : 90.13 % Rotamer Outliers : 0.83 % 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: -2.82 (0.25), residues: 1114 helix: -0.98 (0.23), residues: 524 sheet: -4.55 (0.67), residues: 24 loop : -2.68 (0.26), residues: 566 *********************** 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 138 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 1.057 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 131 average time/residue: 0.1746 time to fit residues: 35.2672 Evaluate side-chains 125 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 121 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0814 time to fit residues: 2.0167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.4980 chunk 50 optimal weight: 5.9990 chunk 73 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 0.1980 chunk 9 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 120 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: 0.8208 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 9071 Z= 0.195 Angle : 0.694 12.368 12286 Z= 0.337 Chirality : 0.042 0.230 1424 Planarity : 0.005 0.072 1519 Dihedral : 6.806 75.640 1233 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer Outliers : 0.62 % 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: -2.78 (0.25), residues: 1114 helix: -0.85 (0.23), residues: 524 sheet: -4.35 (0.73), residues: 24 loop : -2.79 (0.25), residues: 566 ********************** 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 134 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 128 time to evaluate : 1.024 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 5 residues processed: 129 average time/residue: 0.1550 time to fit residues: 30.8386 Evaluate side-chains 126 residues out of total 962 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 1.013 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0817 time to fit residues: 2.1486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 27 optimal weight: 9.9990 chunk 81 optimal weight: 0.0870 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 overall best weight: 5.2166 ------------------------------------------------------------------------------- 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 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** 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 424 GLN A 617 GLN B 617 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.118369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.088300 restraints weight = 17343.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.090768 restraints weight = 10270.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.092516 restraints weight = 7288.970| |-----------------------------------------------------------------------------| r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.078 9071 Z= 0.483 Angle : 0.889 13.383 12286 Z= 0.446 Chirality : 0.050 0.232 1424 Planarity : 0.007 0.163 1519 Dihedral : 7.258 83.708 1233 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 12.75 % Favored : 87.16 % Rotamer Outliers : 0.94 % 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: -3.21 (0.24), residues: 1114 helix: -1.21 (0.22), residues: 526 sheet: -4.79 (0.52), residues: 36 loop : -2.93 (0.25), residues: 552 =============================================================================== Job complete usr+sys time: 1554.45 seconds wall clock time: 29 minutes 16.75 seconds (1756.75 seconds total)