Starting phenix.real_space_refine on Wed Feb 14 04:23:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/02_2024/7wiw_32538_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/02_2024/7wiw_32538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/02_2024/7wiw_32538.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/02_2024/7wiw_32538.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/02_2024/7wiw_32538_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wiw_32538/02_2024/7wiw_32538_updated.pdb" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 3 5.21 5 S 15 5.16 5 C 5473 2.51 5 N 1547 2.21 5 O 1559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 12": "OD1" <-> "OD2" Residue "B PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ASP 95": "OD1" <-> "OD2" Residue "B ASP 103": "OD1" <-> "OD2" Residue "B PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 179": "NH1" <-> "NH2" Residue "B ARG 180": "NH1" <-> "NH2" Residue "B ASP 182": "OD1" <-> "OD2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B GLU 198": "OE1" <-> "OE2" Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 207": "NH1" <-> "NH2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B ARG 232": "NH1" <-> "NH2" Residue "B TYR 283": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 298": "OE1" <-> "OE2" Residue "B ARG 324": "NH1" <-> "NH2" Residue "B ASP 336": "OD1" <-> "OD2" Residue "B TYR 341": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 350": "OD1" <-> "OD2" Residue "B ARG 424": "NH1" <-> "NH2" Residue "B PHE 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 447": "NH1" <-> "NH2" Residue "B ARG 454": "NH1" <-> "NH2" Residue "B ARG 482": "NH1" <-> "NH2" Residue "B ASP 501": "OD1" <-> "OD2" Residue "B GLU 503": "OE1" <-> "OE2" Residue "B ARG 527": "NH1" <-> "NH2" Residue "B ARG 532": "NH1" <-> "NH2" Residue "B ASP 535": "OD1" <-> "OD2" Residue "B PHE 539": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 542": "OD1" <-> "OD2" Residue "B ARG 544": "NH1" <-> "NH2" Residue "B PHE 561": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 566": "NH1" <-> "NH2" Residue "A ARG 284": "NH1" <-> "NH2" Residue "A ARG 329": "NH1" <-> "NH2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A ASP 397": "OD1" <-> "OD2" Residue "A ASP 430": "OD1" <-> "OD2" Residue "A PHE 438": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 464": "NH1" <-> "NH2" Residue "A TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 478": "OE1" <-> "OE2" Residue "A ARG 496": "NH1" <-> "NH2" Residue "A GLU 499": "OE1" <-> "OE2" Residue "A ARG 509": "NH1" <-> "NH2" Residue "A ARG 523": "NH1" <-> "NH2" Residue "A ARG 543": "NH1" <-> "NH2" Residue "A PHE 552": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 595": "NH1" <-> "NH2" Residue "A ARG 599": "NH1" <-> "NH2" Residue "A GLU 600": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A PHE 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 628": "OD1" <-> "OD2" Residue "A ARG 658": "NH1" <-> "NH2" Residue "A ASP 673": "OD1" <-> "OD2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A PHE 688": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 702": "OE1" <-> "OE2" Residue "A GLU 714": "OE1" <-> "OE2" Residue "A ARG 721": "NH1" <-> "NH2" Residue "A GLU 722": "OE1" <-> "OE2" Residue "A ARG 728": "NH1" <-> "NH2" Residue "A ARG 753": "NH1" <-> "NH2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ASP 770": "OD1" <-> "OD2" Residue "A PHE 775": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 777": "OD1" <-> "OD2" Residue "A ARG 793": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ASP 811": "OD1" <-> "OD2" Residue "A ARG 836": "NH1" <-> "NH2" Residue "A TYR 837": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 839": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8603 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 4198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4198 Classifications: {'peptide': 567} Link IDs: {'PTRANS': 25, 'TRANS': 541} Chain: "A" Number of atoms: 4340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 570, 4340 Classifications: {'peptide': 570} Link IDs: {'PTRANS': 25, 'TRANS': 544} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.85, per 1000 atoms: 0.56 Number of scatterers: 8603 At special positions: 0 Unit cell: (66.42, 91.02, 137.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 15 16.00 P 6 15.00 Mg 3 11.99 O 1559 8.00 N 1547 7.00 C 5473 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: 3.25 Conformation dependent library (CDL) restraints added in 1.8 seconds 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2084 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 6 sheets defined 48.4% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.79 Creating SS restraints... Processing helix chain 'B' and resid 20 through 44 removed outlier: 3.532A pdb=" N PHE B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N LEU B 38 " --> pdb=" O GLY B 34 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N VAL B 39 " --> pdb=" O THR B 35 " (cutoff:3.500A) Proline residue: B 40 - end of helix Processing helix chain 'B' and resid 50 through 53 Processing helix chain 'B' and resid 57 through 82 removed outlier: 3.991A pdb=" N ILE B 79 " --> pdb=" O ALA B 75 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLU B 80 " --> pdb=" O ARG B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 99 Proline residue: B 98 - end of helix Processing helix chain 'B' and resid 107 through 118 removed outlier: 4.056A pdb=" N ALA B 111 " --> pdb=" O ALA B 107 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 112 " --> pdb=" O GLU B 108 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 113 " --> pdb=" O ASN B 109 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 149 Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 154 through 177 removed outlier: 3.743A pdb=" N ALA B 162 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLY B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N VAL B 164 " --> pdb=" O ALA B 160 " (cutoff:3.500A) Proline residue: B 165 - end of helix Processing helix chain 'B' and resid 179 through 201 Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 218 through 265 removed outlier: 3.833A pdb=" N ALA B 222 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ILE B 238 " --> pdb=" O LEU B 234 " (cutoff:3.500A) Proline residue: B 239 - end of helix Processing helix chain 'B' and resid 270 through 311 removed outlier: 3.748A pdb=" N ALA B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 278 " --> pdb=" O ILE B 274 " (cutoff:3.500A) Proline residue: B 286 - end of helix removed outlier: 3.849A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLU B 292 " --> pdb=" O THR B 288 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Proline residue: B 295 - end of helix Processing helix chain 'B' and resid 375 through 380 Processing helix chain 'B' and resid 397 through 399 No H-bonds generated for 'chain 'B' and resid 397 through 399' Processing helix chain 'B' and resid 423 through 428 Processing helix chain 'B' and resid 436 through 445 Processing helix chain 'B' and resid 449 through 454 Processing helix chain 'B' and resid 472 through 484 removed outlier: 3.631A pdb=" N GLN B 476 " --> pdb=" O GLY B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 514 removed outlier: 3.520A pdb=" N ALA B 506 " --> pdb=" O ALA B 502 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ALA B 507 " --> pdb=" O GLU B 503 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 554 No H-bonds generated for 'chain 'B' and resid 551 through 554' Processing helix chain 'B' and resid 560 through 563 No H-bonds generated for 'chain 'B' and resid 560 through 563' Processing helix chain 'A' and resid 309 through 323 removed outlier: 3.631A pdb=" N GLU A 316 " --> pdb=" O VAL A 312 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N VAL A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N SER A 323 " --> pdb=" O ARG A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 349 removed outlier: 4.261A pdb=" N THR A 332 " --> pdb=" O HIS A 328 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N VAL A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA A 336 " --> pdb=" O THR A 332 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA A 337 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY A 339 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LEU A 340 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LEU A 341 " --> pdb=" O ALA A 337 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLY A 342 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 348 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ALA A 349 " --> pdb=" O ALA A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 373 removed outlier: 3.780A pdb=" N HIS A 356 " --> pdb=" O THR A 352 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 362 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG A 369 " --> pdb=" O ALA A 365 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LEU A 371 " --> pdb=" O ARG A 367 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N SER A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 385 removed outlier: 3.935A pdb=" N THR A 383 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N SER A 384 " --> pdb=" O TRP A 381 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 385 " --> pdb=" O PHE A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 395 removed outlier: 3.593A pdb=" N LEU A 393 " --> pdb=" O SER A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 405 No H-bonds generated for 'chain 'A' and resid 402 through 405' Processing helix chain 'A' and resid 409 through 417 removed outlier: 4.121A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N VAL A 417 " --> pdb=" O VAL A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 422 No H-bonds generated for 'chain 'A' and resid 419 through 422' Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.740A pdb=" N VAL A 429 " --> pdb=" O TYR A 425 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 425 through 429' Processing helix chain 'A' and resid 431 through 434 No H-bonds generated for 'chain 'A' and resid 431 through 434' Processing helix chain 'A' and resid 438 through 452 removed outlier: 3.511A pdb=" N THR A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N LEU A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR A 452 " --> pdb=" O THR A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 477 removed outlier: 3.561A pdb=" N GLU A 467 " --> pdb=" O GLN A 463 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LYS A 468 " --> pdb=" O ARG A 464 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLU A 472 " --> pdb=" O LYS A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 483 No H-bonds generated for 'chain 'A' and resid 480 through 483' Processing helix chain 'A' and resid 491 through 514 removed outlier: 3.554A pdb=" N ARG A 496 " --> pdb=" O SER A 492 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP A 498 " --> pdb=" O ARG A 494 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N GLU A 499 " --> pdb=" O ARG A 495 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N TYR A 500 " --> pdb=" O ARG A 496 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 506 " --> pdb=" O GLY A 502 " (cutoff:3.500A) Proline residue: A 510 - end of helix removed outlier: 3.846A pdb=" N GLY A 513 " --> pdb=" O ARG A 509 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LYS A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 520 No H-bonds generated for 'chain 'A' and resid 517 through 520' Processing helix chain 'A' and resid 524 through 538 removed outlier: 3.566A pdb=" N TRP A 529 " --> pdb=" O ALA A 525 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ALA A 532 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 538 " --> pdb=" O THR A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 550 through 553 No H-bonds generated for 'chain 'A' and resid 550 through 553' Processing helix chain 'A' and resid 559 through 567 Processing helix chain 'A' and resid 570 through 586 removed outlier: 3.693A pdb=" N LEU A 577 " --> pdb=" O LEU A 573 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN A 584 " --> pdb=" O ALA A 580 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR A 586 " --> pdb=" O HIS A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 716 through 722 Processing helix chain 'A' and resid 726 through 731 removed outlier: 3.686A pdb=" N ARG A 731 " --> pdb=" O ASP A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 737 No H-bonds generated for 'chain 'A' and resid 735 through 737' Processing helix chain 'A' and resid 753 through 760 removed outlier: 3.516A pdb=" N ALA A 757 " --> pdb=" O ARG A 753 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA A 759 " --> pdb=" O THR A 755 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'B' and resid 332 through 335 Processing sheet with id= B, first strand: chain 'B' and resid 544 through 549 removed outlier: 7.190A pdb=" N PHE B 539 " --> pdb=" O VAL B 546 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N ASP B 548 " --> pdb=" O VAL B 537 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N VAL B 537 " --> pdb=" O ASP B 548 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA B 363 " --> pdb=" O LEU B 538 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL B 540 " --> pdb=" O ALA B 363 " (cutoff:3.500A) removed outlier: 6.169A pdb=" N VAL B 365 " --> pdb=" O VAL B 540 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N SER B 410 " --> pdb=" O LEU B 492 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 337 through 339 removed outlier: 7.476A pdb=" N PHE B 339 " --> pdb=" O ASP B 350 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ASP B 350 " --> pdb=" O PHE B 339 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 686 through 689 removed outlier: 6.916A pdb=" N VAL A 766 " --> pdb=" O GLY A 687 " (cutoff:3.500A) removed outlier: 8.313A pdb=" N VAL A 689 " --> pdb=" O VAL A 766 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 768 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N THR A 796 " --> pdb=" O LEU A 767 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU A 769 " --> pdb=" O THR A 796 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N LEU A 798 " --> pdb=" O LEU A 769 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'A' and resid 615 through 617 removed outlier: 7.618A pdb=" N PHE A 617 " --> pdb=" O GLN A 627 " (cutoff:3.500A) removed outlier: 5.435A pdb=" N GLN A 627 " --> pdb=" O PHE A 617 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 813 through 817 removed outlier: 4.160A pdb=" N GLU A 823 " --> pdb=" O VAL A 815 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ASP A 817 " --> pdb=" O ILE A 821 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE A 821 " --> pdb=" O ASP A 817 " (cutoff:3.500A) 301 hydrogen bonds defined for protein. 879 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: 2.36 Time building geometry restraints manager: 3.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.28: 1385 1.28 - 1.41: 2087 1.41 - 1.54: 5245 1.54 - 1.67: 22 1.67 - 1.81: 25 Bond restraints: 8764 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.06e+01 bond pdb=" C4 ATP A 901 " pdb=" C5 ATP A 901 " ideal model delta sigma weight residual 1.388 1.465 -0.077 1.00e-02 1.00e+04 5.95e+01 bond pdb=" C VAL B 493 " pdb=" O VAL B 493 " ideal model delta sigma weight residual 1.238 1.152 0.085 1.17e-02 7.31e+03 5.31e+01 bond pdb=" C5 ATP A 901 " pdb=" C6 ATP A 901 " ideal model delta sigma weight residual 1.409 1.478 -0.069 1.00e-02 1.00e+04 4.76e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.38e+01 ... (remaining 8759 not shown) Histogram of bond angle deviations from ideal: 99.92 - 107.18: 307 107.18 - 114.43: 5284 114.43 - 121.69: 4345 121.69 - 128.94: 1966 128.94 - 136.20: 82 Bond angle restraints: 11984 Sorted by residual: angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 119.13 20.74 1.00e+00 1.00e+00 4.30e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 122.08 14.75 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 118.68 8.12 1.00e+00 1.00e+00 6.60e+01 angle pdb=" C5 ATP A 901 " pdb=" C4 ATP A 901 " pdb=" N3 ATP A 901 " ideal model delta sigma weight residual 126.80 118.76 8.04 1.00e+00 1.00e+00 6.46e+01 angle pdb=" PB ATP A 901 " pdb=" O3B ATP A 901 " pdb=" PG ATP A 901 " ideal model delta sigma weight residual 139.87 132.41 7.46 1.00e+00 1.00e+00 5.56e+01 ... (remaining 11979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 4719 17.73 - 35.46: 390 35.46 - 53.19: 92 53.19 - 70.92: 17 70.92 - 88.65: 10 Dihedral angle restraints: 5228 sinusoidal: 1995 harmonic: 3233 Sorted by residual: dihedral pdb=" CA ALA A 711 " pdb=" C ALA A 711 " pdb=" N PRO A 712 " pdb=" CA PRO A 712 " ideal model delta harmonic sigma weight residual 180.00 -152.63 -27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA PRO A 712 " pdb=" C PRO A 712 " pdb=" N ALA A 713 " pdb=" CA ALA A 713 " ideal model delta harmonic sigma weight residual 180.00 157.75 22.25 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" N VAL B 493 " pdb=" C VAL B 493 " pdb=" CA VAL B 493 " pdb=" CB VAL B 493 " ideal model delta harmonic sigma weight residual 123.40 113.54 9.86 0 2.50e+00 1.60e-01 1.55e+01 ... (remaining 5225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1381 0.091 - 0.182: 71 0.182 - 0.272: 5 0.272 - 0.363: 1 0.363 - 0.454: 2 Chirality restraints: 1460 Sorted by residual: chirality pdb=" CB VAL B 328 " pdb=" CA VAL B 328 " pdb=" CG1 VAL B 328 " pdb=" CG2 VAL B 328 " both_signs ideal model delta sigma weight residual False -2.63 -2.18 -0.45 2.00e-01 2.50e+01 5.16e+00 chirality pdb=" CA VAL B 493 " pdb=" N VAL B 493 " pdb=" C VAL B 493 " pdb=" CB VAL B 493 " both_signs ideal model delta sigma weight residual False 2.44 2.86 -0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ASP B 325 " pdb=" N ASP B 325 " pdb=" C ASP B 325 " pdb=" CB ASP B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 1457 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA HIS A 827 " 0.019 2.00e-02 2.50e+03 3.73e-02 1.39e+01 pdb=" C HIS A 827 " -0.065 2.00e-02 2.50e+03 pdb=" O HIS A 827 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU A 828 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 402 " 0.018 2.00e-02 2.50e+03 3.71e-02 1.37e+01 pdb=" C HIS A 402 " -0.064 2.00e-02 2.50e+03 pdb=" O HIS A 402 " 0.024 2.00e-02 2.50e+03 pdb=" N TYR A 403 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 324 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C ARG B 324 " 0.058 2.00e-02 2.50e+03 pdb=" O ARG B 324 " -0.022 2.00e-02 2.50e+03 pdb=" N ASP B 325 " -0.019 2.00e-02 2.50e+03 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 54 2.49 - 3.09: 6082 3.09 - 3.70: 12738 3.70 - 4.30: 19043 4.30 - 4.90: 32272 Nonbonded interactions: 70189 Sorted by model distance: nonbonded pdb=" OE1 GLN B 414 " pdb="MG MG B 602 " model vdw 1.891 2.170 nonbonded pdb=" OE1 GLN A 691 " pdb="MG MG A 902 " model vdw 1.895 2.170 nonbonded pdb=" OG SER A 650 " pdb="MG MG A 902 " model vdw 1.987 2.170 nonbonded pdb=" OG SER B 373 " pdb="MG MG B 602 " model vdw 2.110 2.170 nonbonded pdb=" O2B ATP B 601 " pdb="MG MG B 602 " model vdw 2.132 2.170 ... (remaining 70184 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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.060 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: 12.250 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.310 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 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 0.085 8764 Z= 0.402 Angle : 0.987 20.743 11984 Z= 0.666 Chirality : 0.049 0.454 1460 Planarity : 0.006 0.075 1522 Dihedral : 14.745 88.649 3144 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.62 % Allowed : 7.06 % Favored : 92.32 % Rotamer: Outliers : 1.03 % Allowed : 6.86 % Favored : 92.11 % Cbeta Deviations : 0.10 % 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: -4.54 (0.21), residues: 1133 helix: -2.55 (0.17), residues: 701 sheet: -2.40 (0.84), residues: 33 loop : -3.70 (0.24), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 154 HIS 0.009 0.001 HIS A 407 PHE 0.011 0.001 PHE B 199 TYR 0.010 0.001 TYR B 283 ARG 0.002 0.000 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 95 time to evaluate : 0.984 Fit side-chains REVERT: A 407 HIS cc_start: 0.8931 (OUTLIER) cc_final: 0.8412 (p90) REVERT: A 714 GLU cc_start: 0.7495 (tm-30) cc_final: 0.7028 (tm-30) outliers start: 9 outliers final: 3 residues processed: 101 average time/residue: 0.2887 time to fit residues: 37.5422 Evaluate side-chains 77 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 495 GLN Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 630 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.0060 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 chunk 102 optimal weight: 0.7980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 109 ASN B 203 GLN B 420 HIS B 438 GLN B 476 GLN B 526 HIS ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 717 GLN A 827 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8764 Z= 0.174 Angle : 0.597 8.157 11984 Z= 0.305 Chirality : 0.041 0.153 1460 Planarity : 0.005 0.078 1522 Dihedral : 9.093 85.808 1313 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.06 % Favored : 92.67 % Rotamer: Outliers : 1.72 % Allowed : 11.21 % Favored : 87.07 % 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: -3.18 (0.24), residues: 1133 helix: -1.51 (0.20), residues: 690 sheet: -2.09 (0.80), residues: 45 loop : -3.03 (0.26), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 154 HIS 0.002 0.001 HIS A 407 PHE 0.015 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.003 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.942 Fit side-chains REVERT: A 286 LEU cc_start: 0.8743 (pp) cc_final: 0.8531 (pp) REVERT: A 714 GLU cc_start: 0.7415 (tm-30) cc_final: 0.6983 (tm-30) outliers start: 15 outliers final: 8 residues processed: 96 average time/residue: 0.2213 time to fit residues: 29.5173 Evaluate side-chains 81 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 766 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.9990 chunk 31 optimal weight: 0.0270 chunk 85 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 0.0270 chunk 111 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 504 ASN ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 752 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8764 Z= 0.153 Angle : 0.559 7.830 11984 Z= 0.283 Chirality : 0.040 0.133 1460 Planarity : 0.005 0.074 1522 Dihedral : 8.353 85.319 1309 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.35 % Favored : 93.38 % Rotamer: Outliers : 2.52 % Allowed : 13.73 % Favored : 83.75 % 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: -2.44 (0.25), residues: 1133 helix: -0.94 (0.21), residues: 685 sheet: -1.12 (0.84), residues: 32 loop : -2.72 (0.26), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.013 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.002 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 77 time to evaluate : 0.858 Fit side-chains outliers start: 22 outliers final: 14 residues processed: 92 average time/residue: 0.2143 time to fit residues: 27.9475 Evaluate side-chains 83 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 69 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 438 GLN Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 422 VAL Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 662 VAL Chi-restraints excluded: chain A residue 766 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN B 383 HIS ** A 480 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.1585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8764 Z= 0.220 Angle : 0.576 7.398 11984 Z= 0.290 Chirality : 0.041 0.140 1460 Planarity : 0.005 0.070 1522 Dihedral : 8.510 88.748 1309 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.26 % Allowed : 7.06 % Favored : 92.67 % Rotamer: Outliers : 2.52 % Allowed : 15.33 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.25), residues: 1133 helix: -0.83 (0.21), residues: 700 sheet: -0.59 (0.88), residues: 32 loop : -2.59 (0.26), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.018 0.001 PHE A 612 TYR 0.010 0.001 TYR B 283 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.969 Fit side-chains outliers start: 22 outliers final: 15 residues processed: 92 average time/residue: 0.2091 time to fit residues: 26.9333 Evaluate side-chains 89 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 74 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 81 optimal weight: 0.6980 chunk 45 optimal weight: 0.0000 chunk 93 optimal weight: 0.6980 chunk 75 optimal weight: 4.9990 chunk 0 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 98 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 overall best weight: 0.4762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 438 GLN A 480 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8764 Z= 0.150 Angle : 0.537 7.303 11984 Z= 0.269 Chirality : 0.040 0.130 1460 Planarity : 0.004 0.070 1522 Dihedral : 8.102 88.798 1309 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.18 % Favored : 93.56 % Rotamer: Outliers : 1.95 % Allowed : 15.90 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.25), residues: 1133 helix: -0.54 (0.22), residues: 693 sheet: -0.07 (0.91), residues: 32 loop : -2.53 (0.26), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.013 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 0.867 Fit side-chains outliers start: 17 outliers final: 14 residues processed: 96 average time/residue: 0.2137 time to fit residues: 28.8317 Evaluate side-chains 89 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.0000 chunk 36 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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: 0.8552 moved from start: 0.1969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8764 Z= 0.163 Angle : 0.540 7.295 11984 Z= 0.270 Chirality : 0.040 0.133 1460 Planarity : 0.004 0.067 1522 Dihedral : 8.039 89.539 1309 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.53 % Favored : 93.20 % Rotamer: Outliers : 3.09 % Allowed : 15.45 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.25), residues: 1133 helix: -0.30 (0.22), residues: 682 sheet: 0.34 (0.95), residues: 32 loop : -2.49 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.014 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 79 time to evaluate : 1.012 Fit side-chains outliers start: 27 outliers final: 21 residues processed: 99 average time/residue: 0.2386 time to fit residues: 32.6938 Evaluate side-chains 99 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 78 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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: 0.8572 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8764 Z= 0.196 Angle : 0.555 8.061 11984 Z= 0.276 Chirality : 0.041 0.138 1460 Planarity : 0.004 0.063 1522 Dihedral : 8.176 87.318 1309 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.53 % Favored : 93.20 % Rotamer: Outliers : 2.75 % Allowed : 16.13 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.25), residues: 1133 helix: -0.24 (0.22), residues: 682 sheet: 0.46 (0.96), residues: 32 loop : -2.45 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 507 HIS 0.003 0.001 HIS A 407 PHE 0.017 0.001 PHE A 612 TYR 0.010 0.001 TYR B 283 ARG 0.001 0.000 ARG B 301 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.940 Fit side-chains outliers start: 24 outliers final: 19 residues processed: 92 average time/residue: 0.2068 time to fit residues: 26.8859 Evaluate side-chains 96 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 77 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 69 optimal weight: 0.0040 chunk 74 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 overall best weight: 0.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 752 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8764 Z= 0.179 Angle : 0.548 7.985 11984 Z= 0.271 Chirality : 0.041 0.142 1460 Planarity : 0.004 0.060 1522 Dihedral : 8.142 87.043 1309 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.35 % Favored : 93.38 % Rotamer: Outliers : 2.86 % Allowed : 16.02 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.26), residues: 1133 helix: -0.11 (0.22), residues: 678 sheet: 0.39 (0.92), residues: 38 loop : -2.45 (0.26), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.015 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.001 0.000 ARG B 544 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 78 time to evaluate : 0.971 Fit side-chains outliers start: 25 outliers final: 22 residues processed: 95 average time/residue: 0.2140 time to fit residues: 28.3849 Evaluate side-chains 97 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 542 ASP Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 0.8980 chunk 104 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 79 optimal weight: 0.1980 chunk 31 optimal weight: 0.7980 chunk 91 optimal weight: 0.9990 chunk 95 optimal weight: 0.0000 chunk 66 optimal weight: 0.4980 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- 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: 0.8518 moved from start: 0.2284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8764 Z= 0.139 Angle : 0.526 7.640 11984 Z= 0.259 Chirality : 0.039 0.137 1460 Planarity : 0.004 0.059 1522 Dihedral : 7.813 88.487 1309 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.74 % Favored : 94.00 % Rotamer: Outliers : 2.63 % Allowed : 16.59 % Favored : 80.78 % 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: -1.23 (0.26), residues: 1133 helix: 0.06 (0.22), residues: 679 sheet: 0.12 (0.89), residues: 45 loop : -2.41 (0.26), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 154 HIS 0.003 0.000 HIS A 407 PHE 0.012 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.001 0.000 ARG A 599 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 0.911 Fit side-chains outliers start: 23 outliers final: 18 residues processed: 93 average time/residue: 0.1899 time to fit residues: 25.5399 Evaluate side-chains 88 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 3.9990 chunk 74 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 0.0070 chunk 27 optimal weight: 0.8980 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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: 0.8538 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8764 Z= 0.163 Angle : 0.539 8.081 11984 Z= 0.264 Chirality : 0.040 0.137 1460 Planarity : 0.004 0.059 1522 Dihedral : 7.887 89.737 1309 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.26 % Allowed : 6.18 % Favored : 93.56 % Rotamer: Outliers : 2.17 % Allowed : 17.28 % Favored : 80.55 % 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: -1.10 (0.26), residues: 1133 helix: 0.16 (0.22), residues: 677 sheet: 0.17 (0.88), residues: 45 loop : -2.33 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.015 0.001 PHE A 612 TYR 0.009 0.001 TYR B 283 ARG 0.001 0.000 ARG B 301 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2266 Ramachandran restraints generated. 1133 Oldfield, 0 Emsley, 1133 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 71 time to evaluate : 1.030 Fit side-chains outliers start: 19 outliers final: 18 residues processed: 84 average time/residue: 0.2013 time to fit residues: 24.5605 Evaluate side-chains 88 residues out of total 874 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 70 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 79 ILE Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 250 LEU Chi-restraints excluded: chain B residue 457 ASP Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain A residue 286 LEU Chi-restraints excluded: chain A residue 291 LEU Chi-restraints excluded: chain A residue 319 ARG Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 407 HIS Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 766 VAL Chi-restraints excluded: chain A residue 816 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 0.0170 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.1980 chunk 78 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.096959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.085121 restraints weight = 13791.997| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 1.83 r_work: 0.2921 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8764 Z= 0.158 Angle : 0.539 8.079 11984 Z= 0.263 Chirality : 0.040 0.138 1460 Planarity : 0.004 0.057 1522 Dihedral : 7.870 88.529 1309 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.26 % Allowed : 5.91 % Favored : 93.82 % Rotamer: Outliers : 2.06 % Allowed : 17.51 % Favored : 80.43 % 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: -0.97 (0.26), residues: 1133 helix: 0.27 (0.22), residues: 677 sheet: 0.24 (0.87), residues: 45 loop : -2.30 (0.26), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 154 HIS 0.003 0.001 HIS A 407 PHE 0.014 0.001 PHE A 612 TYR 0.008 0.001 TYR B 283 ARG 0.001 0.000 ARG A 495 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2037.75 seconds wall clock time: 37 minutes 59.66 seconds (2279.66 seconds total)