Starting phenix.real_space_refine (version: dev) on Sun Dec 11 22:08:20 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/12_2022/5u1d_8482.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/12_2022/5u1d_8482.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.97 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/12_2022/5u1d_8482.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/12_2022/5u1d_8482.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/12_2022/5u1d_8482.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5u1d_8482/12_2022/5u1d_8482.pdb" } resolution = 3.97 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= 0.036 sd= 0.252 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 ARG 312": "NH1" <-> "NH2" Residue "A GLU 396": "OE1" <-> "OE2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "B ARG 140": "NH1" <-> "NH2" Residue "B ARG 252": "NH1" <-> "NH2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B GLU 307": "OE1" <-> "OE2" Residue "B ARG 373": "NH1" <-> "NH2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "B ARG 619": "NH1" <-> "NH2" Residue "X GLU 6": "OE1" <-> "OE2" Residue "X ARG 20": "NH1" <-> "NH2" Residue "X ARG 41": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 7815 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 561, 3635 Classifications: {'peptide': 561} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PTRANS': 18, 'TRANS': 542} Chain breaks: 2 Unresolved chain link angles: 13 Unresolved non-hydrogen bonds: 744 Unresolved non-hydrogen angles: 962 Unresolved non-hydrogen dihedrals: 594 Unresolved non-hydrogen chiralities: 81 Planarities with less than four sites: {'GLN:plan1': 26, 'ASP:plan': 9, 'TYR:plan': 8, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 6, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 11} Unresolved non-hydrogen planarities: 411 Chain: "B" Number of atoms: 3732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 3732 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 186} Link IDs: {'PTRANS': 20, 'TRANS': 531} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 612 Unresolved non-hydrogen angles: 790 Unresolved non-hydrogen dihedrals: 478 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLN:plan1': 25, 'HIS:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 4, 'GLU:plan': 12, 'ARG:plan': 8} Unresolved non-hydrogen planarities: 327 Chain: "X" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 448 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG A 529 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG A 529 " occ=0.50 residue: pdb=" N ARG B 494 " occ=0.50 ... (3 atoms not shown) pdb=" CB ARG B 494 " occ=0.50 Time building chain proxies: 5.38, per 1000 atoms: 0.69 Number of scatterers: 7815 At special positions: 0 Unit cell: (92.8618, 120.53, 116.905, 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 31 16.00 O 1458 8.00 N 1426 7.00 C 4900 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.18 Conformation dependent library (CDL) restraints added in 1.4 seconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2158 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 5 sheets defined 73.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 173 through 181 Processing helix chain 'A' and resid 185 through 202 removed outlier: 4.083A pdb=" N GLY A 200 " --> pdb=" O LEU A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.637A pdb=" N PHE A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 271 removed outlier: 3.871A pdb=" N PHE A 224 " --> pdb=" O SER A 220 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL A 268 " --> pdb=" O VAL A 264 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 269 " --> pdb=" O PHE A 265 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 removed outlier: 4.230A pdb=" N PHE A 276 " --> pdb=" O GLU A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 287 removed outlier: 4.009A pdb=" N ILE A 284 " --> pdb=" O GLN A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 320 removed outlier: 3.564A pdb=" N LEU A 305 " --> pdb=" O GLU A 301 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL A 311 " --> pdb=" O LEU A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 373 removed outlier: 3.648A pdb=" N ILE A 333 " --> pdb=" O MET A 329 " (cutoff:3.500A) Proline residue: A 336 - end of helix removed outlier: 4.223A pdb=" N LEU A 341 " --> pdb=" O LEU A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix removed outlier: 4.023A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LEU A 352 " --> pdb=" O TRP A 348 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A 353 " --> pdb=" O TYR A 349 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N GLN A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.659A pdb=" N VAL A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 380 " --> pdb=" O THR A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 437 removed outlier: 3.640A pdb=" N ALA A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLN A 388 " --> pdb=" O GLU A 384 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLN A 402 " --> pdb=" O LYS A 398 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLY A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N MET A 420 " --> pdb=" O SER A 416 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 433 " --> pdb=" O ILE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 462 removed outlier: 3.809A pdb=" N VAL A 460 " --> pdb=" O GLN A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 483 removed outlier: 4.162A pdb=" N ARG A 467 " --> pdb=" O SER A 463 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLY A 473 " --> pdb=" O GLN A 469 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 477 " --> pdb=" O GLY A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 553 removed outlier: 3.505A pdb=" N ALA A 548 " --> pdb=" O LYS A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 572 Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 594 through 600 Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 628 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.751A pdb=" N THR A 634 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.055A pdb=" N ARG A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS A 660 " --> pdb=" O ALA A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 686 Processing helix chain 'A' and resid 688 through 694 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.662A pdb=" N VAL A 706 " --> pdb=" O HIS A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 725 through 733 Processing helix chain 'A' and resid 734 through 742 Processing helix chain 'B' and resid 131 through 145 removed outlier: 3.648A pdb=" N LYS B 143 " --> pdb=" O TRP B 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU B 144 " --> pdb=" O ARG B 140 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 removed outlier: 4.073A pdb=" N LEU B 152 " --> pdb=" O ASP B 148 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 183 removed outlier: 4.414A pdb=" N HIS B 171 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLY B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 236 removed outlier: 3.678A pdb=" N GLY B 211 " --> pdb=" O ALA B 207 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER B 219 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 235 " --> pdb=" O SER B 231 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 236 " --> pdb=" O SER B 232 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 4.134A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLN B 242 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU B 243 " --> pdb=" O GLY B 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 289 removed outlier: 4.797A pdb=" N THR B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR B 258 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU B 264 " --> pdb=" O MET B 260 " (cutoff:3.500A) Proline residue: B 265 - end of helix removed outlier: 3.549A pdb=" N ILE B 288 " --> pdb=" O PHE B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 299 removed outlier: 3.791A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 338 removed outlier: 3.685A pdb=" N ALA B 306 " --> pdb=" O PHE B 302 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 309 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU B 316 " --> pdb=" O THR B 312 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 332 " --> pdb=" O ALA B 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 346 Processing helix chain 'B' and resid 347 through 401 removed outlier: 3.538A pdb=" N GLN B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LEU B 365 " --> pdb=" O GLN B 361 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR B 366 " --> pdb=" O CYS B 362 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N CYS B 394 " --> pdb=" O LEU B 390 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 399 " --> pdb=" O GLY B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 433 removed outlier: 3.790A pdb=" N LEU B 409 " --> pdb=" O THR B 405 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N LEU B 410 " --> pdb=" O GLN B 406 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLY B 420 " --> pdb=" O GLN B 416 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR B 425 " --> pdb=" O SER B 421 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N TYR B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) Processing helix chain 'B' and resid 436 through 449 removed outlier: 3.896A pdb=" N ALA B 440 " --> pdb=" O ASN B 436 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N LYS B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N MET B 447 " --> pdb=" O VAL B 443 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N ARG B 449 " --> pdb=" O SER B 445 " (cutoff:3.500A) Processing helix chain 'B' and resid 508 through 518 Processing helix chain 'B' and resid 538 through 546 Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 572 through 584 Processing helix chain 'B' and resid 585 through 592 Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 608 through 624 removed outlier: 3.529A pdb=" N ALA B 616 " --> pdb=" O LYS B 612 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 646 removed outlier: 4.359A pdb=" N GLU B 642 " --> pdb=" O ASP B 638 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLN B 643 " --> pdb=" O VAL B 639 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N ALA B 644 " --> pdb=" O GLN B 640 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 647 through 654 removed outlier: 3.760A pdb=" N SER B 650 " --> pdb=" O ASP B 647 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ARG B 654 " --> pdb=" O ARG B 651 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 669 Processing helix chain 'X' and resid 2 through 14 removed outlier: 3.883A pdb=" N GLU X 6 " --> pdb=" O SER X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 44 removed outlier: 3.845A pdb=" N ASP X 24 " --> pdb=" O ARG X 20 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N VAL X 25 " --> pdb=" O THR X 21 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP X 27 " --> pdb=" O ALA X 23 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG X 41 " --> pdb=" O ARG X 37 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL X 44 " --> pdb=" O ALA X 40 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 521 through 527 removed outlier: 5.019A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 7.101A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N PHE A 526 " --> pdb=" O GLN A 506 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N GLN A 506 " --> pdb=" O PHE A 526 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 533 through 535 removed outlier: 6.903A pdb=" N THR A 534 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 5.945A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 714 through 716 removed outlier: 3.727A pdb=" N GLU A 722 " --> pdb=" O PHE A 714 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU A 716 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 486 through 489 removed outlier: 5.093A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 548 through 549 removed outlier: 6.559A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) 584 hydrogen bonds defined for protein. 1707 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: 2.43 Time building geometry restraints manager: 3.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2692 1.34 - 1.46: 649 1.46 - 1.58: 4523 1.58 - 1.69: 0 1.69 - 1.81: 55 Bond restraints: 7919 Sorted by residual: bond pdb=" CA ILE A 204 " pdb=" CB ILE A 204 " ideal model delta sigma weight residual 1.534 1.565 -0.031 6.80e-03 2.16e+04 2.05e+01 bond pdb=" CA ILE A 204 " pdb=" C ILE A 204 " ideal model delta sigma weight residual 1.520 1.545 -0.025 8.80e-03 1.29e+04 8.27e+00 bond pdb=" N LEU A 335 " pdb=" CA LEU A 335 " ideal model delta sigma weight residual 1.462 1.484 -0.023 9.50e-03 1.11e+04 5.67e+00 bond pdb=" N GLY B 524 " pdb=" CA GLY B 524 " ideal model delta sigma weight residual 1.446 1.469 -0.023 9.50e-03 1.11e+04 5.62e+00 bond pdb=" N ASP B 130 " pdb=" CA ASP B 130 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.90e-02 2.77e+03 4.87e+00 ... (remaining 7914 not shown) Histogram of bond angle deviations from ideal: 99.93 - 106.74: 142 106.74 - 113.55: 4166 113.55 - 120.35: 3186 120.35 - 127.16: 3250 127.16 - 133.97: 50 Bond angle restraints: 10794 Sorted by residual: angle pdb=" C ASP B 624 " pdb=" N PRO B 625 " pdb=" CA PRO B 625 " ideal model delta sigma weight residual 120.11 130.50 -10.39 1.12e+00 7.97e-01 8.61e+01 angle pdb=" C SER A 688 " pdb=" N PRO A 689 " pdb=" CA PRO A 689 " ideal model delta sigma weight residual 119.05 129.31 -10.26 1.11e+00 8.12e-01 8.54e+01 angle pdb=" C LYS A 660 " pdb=" N PRO A 661 " pdb=" CA PRO A 661 " ideal model delta sigma weight residual 120.31 128.17 -7.86 9.80e-01 1.04e+00 6.44e+01 angle pdb=" C LEU A 569 " pdb=" N PRO A 570 " pdb=" CA PRO A 570 " ideal model delta sigma weight residual 119.28 127.08 -7.80 1.10e+00 8.26e-01 5.03e+01 angle pdb=" C THR A 495 " pdb=" N PRO A 496 " pdb=" CA PRO A 496 " ideal model delta sigma weight residual 119.84 128.32 -8.48 1.25e+00 6.40e-01 4.60e+01 ... (remaining 10789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.80: 4369 15.80 - 31.60: 210 31.60 - 47.40: 79 47.40 - 63.20: 20 63.20 - 79.00: 1 Dihedral angle restraints: 4679 sinusoidal: 1333 harmonic: 3346 Sorted by residual: dihedral pdb=" CA SER A 182 " pdb=" C SER A 182 " pdb=" N GLU A 183 " pdb=" CA GLU A 183 " ideal model delta harmonic sigma weight residual -180.00 -160.36 -19.64 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU A 183 " pdb=" C GLU A 183 " pdb=" N THR A 184 " pdb=" CA THR A 184 " ideal model delta harmonic sigma weight residual -180.00 -160.78 -19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA THR A 184 " pdb=" C THR A 184 " pdb=" N ARG A 185 " pdb=" CA ARG A 185 " ideal model delta harmonic sigma weight residual 180.00 -160.84 -19.16 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 837 0.038 - 0.076: 297 0.076 - 0.114: 117 0.114 - 0.152: 36 0.152 - 0.190: 14 Chirality restraints: 1301 Sorted by residual: chirality pdb=" CA HIS X 45 " pdb=" N HIS X 45 " pdb=" C HIS X 45 " pdb=" CB HIS X 45 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.01e-01 chirality pdb=" CA ASP A 483 " pdb=" N ASP A 483 " pdb=" C ASP A 483 " pdb=" CB ASP A 483 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.39e-01 chirality pdb=" CA ILE A 204 " pdb=" N ILE A 204 " pdb=" C ILE A 204 " pdb=" CB ILE A 204 " both_signs ideal model delta sigma weight residual False 2.43 2.26 0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 1298 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET B 300 " -0.030 5.00e-02 4.00e+02 4.59e-02 3.38e+00 pdb=" N PRO B 301 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO B 301 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 301 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG B 146 " -0.024 5.00e-02 4.00e+02 3.57e-02 2.04e+00 pdb=" N PRO B 147 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 465 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 466 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 466 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 466 " -0.019 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 3099 2.94 - 3.43: 8317 3.43 - 3.92: 12011 3.92 - 4.41: 12091 4.41 - 4.90: 21589 Nonbonded interactions: 57107 Sorted by model distance: nonbonded pdb=" O GLU A 183 " pdb=" OG1 THR A 184 " model vdw 2.452 2.440 nonbonded pdb=" O MET B 218 " pdb=" OG SER B 261 " model vdw 2.513 2.440 nonbonded pdb=" O ARG X 20 " pdb=" OG1 THR X 21 " model vdw 2.563 2.440 nonbonded pdb=" O SER B 255 " pdb=" OG1 THR B 258 " model vdw 2.571 2.440 nonbonded pdb=" O LEU A 360 " pdb=" OG SER A 363 " model vdw 2.582 2.440 ... (remaining 57102 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 31 5.16 5 C 4900 2.51 5 N 1426 2.21 5 O 1458 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=0.50 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: 1.170 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: 4.820 Check model and map are aligned: 0.120 Convert atoms to be neutral: 0.060 Process input model: 24.890 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4843 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 : 0.007 0.042 7919 Z= 0.493 Angle : 1.173 10.391 10794 Z= 0.861 Chirality : 0.050 0.190 1301 Planarity : 0.003 0.046 1427 Dihedral : 12.049 78.999 2521 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 0.07 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.70 % Favored : 94.13 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.21), residues: 1158 helix: -0.58 (0.15), residues: 765 sheet: -4.63 (0.65), residues: 37 loop : -2.79 (0.29), residues: 356 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 363 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 366 average time/residue: 0.2120 time to fit residues: 100.8781 Evaluate side-chains 274 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 272 time to evaluate : 0.924 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 2 average time/residue: 0.2982 time to fit residues: 1.9733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 46 optimal weight: 20.0000 chunk 90 optimal weight: 30.0000 chunk 35 optimal weight: 30.0000 chunk 55 optimal weight: 6.9990 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 20.0000 overall best weight: 8.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 227 ASN A 251 ASN A 382 ASN A 401 ASN A 469 GLN A 701 GLN ** B 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 267 ASN B 311 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 539 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4895 moved from start: 0.4020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.042 7919 Z= 0.306 Angle : 0.657 10.509 10794 Z= 0.352 Chirality : 0.041 0.182 1301 Planarity : 0.005 0.051 1427 Dihedral : 4.205 19.330 1239 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer Outliers : 8.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1158 helix: 1.42 (0.17), residues: 803 sheet: -4.00 (0.66), residues: 47 loop : -2.28 (0.33), residues: 308 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 256 time to evaluate : 0.954 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 52 outliers final: 36 residues processed: 285 average time/residue: 0.1855 time to fit residues: 71.6793 Evaluate side-chains 272 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 236 time to evaluate : 0.966 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.0869 time to fit residues: 6.5721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 50.0000 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 8.9990 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 20.0000 chunk 104 optimal weight: 6.9990 chunk 35 optimal weight: 50.0000 chunk 84 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 171 HIS ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 452 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4880 moved from start: 0.4625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 7919 Z= 0.231 Angle : 0.576 8.318 10794 Z= 0.299 Chirality : 0.038 0.243 1301 Planarity : 0.004 0.041 1427 Dihedral : 3.902 19.375 1239 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.80 % Favored : 96.11 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.25), residues: 1158 helix: 1.95 (0.18), residues: 803 sheet: -3.63 (0.85), residues: 34 loop : -2.09 (0.33), residues: 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 256 time to evaluate : 0.959 Fit side-chains revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 264 average time/residue: 0.1885 time to fit residues: 66.9651 Evaluate side-chains 253 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 243 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0788 time to fit residues: 2.6891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 30.0000 chunk 11 optimal weight: 10.0000 chunk 50 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 100 optimal weight: 20.0000 chunk 30 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 382 ASN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN B 539 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4870 moved from start: 0.5437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 7919 Z= 0.245 Angle : 0.603 8.259 10794 Z= 0.317 Chirality : 0.039 0.211 1301 Planarity : 0.004 0.039 1427 Dihedral : 4.016 20.049 1239 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.40 % Favored : 95.51 % Rotamer Outliers : 5.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1158 helix: 1.85 (0.18), residues: 804 sheet: -3.43 (0.84), residues: 34 loop : -2.05 (0.33), residues: 320 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 258 time to evaluate : 0.837 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 33 outliers final: 18 residues processed: 269 average time/residue: 0.1902 time to fit residues: 68.9788 Evaluate side-chains 260 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 242 time to evaluate : 0.746 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0711 time to fit residues: 3.5128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 50.0000 chunk 63 optimal weight: 30.0000 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 40.0000 chunk 46 optimal weight: 0.0570 chunk 95 optimal weight: 30.0000 chunk 77 optimal weight: 4.9990 chunk 0 optimal weight: 40.0000 chunk 57 optimal weight: 7.9990 chunk 100 optimal weight: 20.0000 chunk 28 optimal weight: 20.0000 overall best weight: 7.6108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 ASN A 469 GLN ** B 416 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4869 moved from start: 0.5981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 7919 Z= 0.272 Angle : 0.616 8.112 10794 Z= 0.327 Chirality : 0.040 0.187 1301 Planarity : 0.004 0.046 1427 Dihedral : 4.198 21.634 1239 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer Outliers : 3.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.25), residues: 1158 helix: 1.66 (0.18), residues: 808 sheet: -3.32 (0.81), residues: 34 loop : -2.04 (0.33), residues: 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 246 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 23 outliers final: 10 residues processed: 253 average time/residue: 0.1867 time to fit residues: 64.1082 Evaluate side-chains 248 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 238 time to evaluate : 0.857 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0725 time to fit residues: 2.5575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 50.0000 chunk 100 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 93 optimal weight: 40.0000 chunk 51 optimal weight: 9.9990 chunk 9 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 20.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 GLN ** 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: 0.4856 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7919 Z= 0.229 Angle : 0.611 8.836 10794 Z= 0.319 Chirality : 0.038 0.182 1301 Planarity : 0.004 0.033 1427 Dihedral : 4.065 21.889 1239 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer Outliers : 3.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1158 helix: 1.77 (0.18), residues: 804 sheet: -3.48 (0.71), residues: 44 loop : -1.78 (0.34), residues: 310 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 242 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 13 residues processed: 249 average time/residue: 0.1844 time to fit residues: 63.0045 Evaluate side-chains 241 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 228 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.0762 time to fit residues: 3.0529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 81 optimal weight: 20.0000 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 0.6980 chunk 69 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 ASN A 451 GLN B 416 GLN B 424 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4860 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 7919 Z= 0.207 Angle : 0.614 10.344 10794 Z= 0.317 Chirality : 0.038 0.178 1301 Planarity : 0.003 0.033 1427 Dihedral : 3.942 21.992 1239 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 13.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.06 % Favored : 95.85 % Rotamer Outliers : 4.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.25), residues: 1158 helix: 1.87 (0.18), residues: 801 sheet: -3.42 (0.71), residues: 45 loop : -1.67 (0.34), residues: 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 244 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 17 residues processed: 256 average time/residue: 0.1806 time to fit residues: 63.0467 Evaluate side-chains 240 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 223 time to evaluate : 0.911 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.0739 time to fit residues: 3.5023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 76 optimal weight: 30.0000 chunk 55 optimal weight: 8.9990 chunk 10 optimal weight: 7.9990 chunk 87 optimal weight: 4.9990 chunk 101 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 97 optimal weight: 20.0000 chunk 104 optimal weight: 8.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN A 456 GLN B 424 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4852 moved from start: 0.6688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 7919 Z= 0.242 Angle : 0.648 9.065 10794 Z= 0.338 Chirality : 0.040 0.226 1301 Planarity : 0.003 0.031 1427 Dihedral : 4.100 22.880 1239 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.66 % Favored : 95.25 % Rotamer Outliers : 2.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.25), residues: 1158 helix: 1.69 (0.18), residues: 811 sheet: -3.23 (0.73), residues: 45 loop : -1.65 (0.36), residues: 302 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 240 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 9 residues processed: 243 average time/residue: 0.1904 time to fit residues: 62.0597 Evaluate side-chains 236 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 227 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0709 time to fit residues: 2.2874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 40.0000 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 50.0000 chunk 81 optimal weight: 20.0000 chunk 31 optimal weight: 50.0000 chunk 94 optimal weight: 9.9990 chunk 98 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 110 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 overall best weight: 6.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4851 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.056 7919 Z= 0.267 Angle : 0.697 12.724 10794 Z= 0.367 Chirality : 0.042 0.325 1301 Planarity : 0.004 0.037 1427 Dihedral : 4.234 23.727 1239 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.75 % Favored : 95.16 % Rotamer Outliers : 3.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.25), residues: 1158 helix: 1.57 (0.18), residues: 812 sheet: -3.07 (0.73), residues: 45 loop : -1.62 (0.36), residues: 301 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 227 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 18 outliers final: 11 residues processed: 233 average time/residue: 0.1844 time to fit residues: 58.8331 Evaluate side-chains 235 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 224 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.0758 time to fit residues: 2.6847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 chunk 92 optimal weight: 40.0000 chunk 9 optimal weight: 0.0980 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 chunk 28 optimal weight: 8.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 416 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4845 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.051 7919 Z= 0.243 Angle : 0.701 12.786 10794 Z= 0.364 Chirality : 0.041 0.315 1301 Planarity : 0.004 0.039 1427 Dihedral : 4.131 24.650 1239 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1158 helix: 1.65 (0.18), residues: 808 sheet: -2.91 (0.75), residues: 45 loop : -1.53 (0.36), residues: 305 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 237 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 238 average time/residue: 0.1919 time to fit residues: 61.9380 Evaluate side-chains 227 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 225 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0711 time to fit residues: 1.5053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 40.0000 chunk 38 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 11 optimal weight: 20.0000 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 66 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 416 GLN ** 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 = 0.3945 r_free = 0.3945 target = 0.153673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.132690 restraints weight = 19932.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.135698 restraints weight = 13346.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.137915 restraints weight = 9818.165| |-----------------------------------------------------------------------------| r_work (final): 0.3755 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3945 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3945 r_free = 0.3945 target_work(ls_wunit_k1) = 0.154 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3940 r_free = 0.3940 target_work(ls_wunit_k1) = 0.153 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3940 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.7190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 7919 Z= 0.235 Angle : 0.722 13.145 10794 Z= 0.373 Chirality : 0.041 0.297 1301 Planarity : 0.004 0.042 1427 Dihedral : 4.148 26.050 1239 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 15.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.49 % Favored : 95.42 % Rotamer Outliers : 1.18 % 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: 0.91 (0.25), residues: 1158 helix: 1.60 (0.18), residues: 808 sheet: -2.78 (0.77), residues: 45 loop : -1.56 (0.35), residues: 305 =============================================================================== Job complete usr+sys time: 2354.44 seconds wall clock time: 42 minutes 36.29 seconds (2556.29 seconds total)