Starting phenix.real_space_refine on Fri Jul 19 12:35:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4j_41033/07_2024/8t4j_41033.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4j_41033/07_2024/8t4j_41033.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4j_41033/07_2024/8t4j_41033.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4j_41033/07_2024/8t4j_41033.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4j_41033/07_2024/8t4j_41033.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t4j_41033/07_2024/8t4j_41033.cif" } resolution = 3.9 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 32 5.16 5 C 4956 2.51 5 N 1374 2.21 5 O 1462 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 237": "OD1" <-> "OD2" Residue "B GLU 243": "OE1" <-> "OE2" Residue "B ASP 256": "OD1" <-> "OD2" Residue "B GLU 316": "OE1" <-> "OE2" Residue "B PHE 345": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 417": "OE1" <-> "OE2" Residue "B TYR 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 602": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 242": "OE1" <-> "OE2" Residue "A PHE 243": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 246": "OD1" <-> "OD2" Residue "A PHE 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 301": "OE1" <-> "OE2" Residue "A PHE 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 358": "OE1" <-> "OE2" Residue "A TYR 450": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 7824 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 547, 4190 Classifications: {'peptide': 547} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 20, 'TRANS': 526} Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 120 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 66 Chain: "A" Number of atoms: 3567 Number of conformers: 1 Conformer: "" Number of residues, atoms: 552, 3567 Classifications: {'peptide': 552} Incomplete info: {'truncation_to_alanine': 202} Link IDs: {'PTRANS': 18, 'TRANS': 533} Chain breaks: 2 Unresolved non-hydrogen bonds: 722 Unresolved non-hydrogen angles: 930 Unresolved non-hydrogen dihedrals: 574 Unresolved non-hydrogen chiralities: 80 Planarities with less than four sites: {'GLN:plan1': 24, 'HIS:plan': 7, 'TYR:plan': 9, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 19, 'ARG:plan': 13} Unresolved non-hydrogen planarities: 422 Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 67 Classifications: {'peptide': 8} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 6} Chain breaks: 1 Time building chain proxies: 5.77, per 1000 atoms: 0.74 Number of scatterers: 7824 At special positions: 0 Unit cell: (74.671, 114.104, 132.562, 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 32 16.00 O 1462 8.00 N 1374 7.00 C 4956 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: 3.24 Conformation dependent library (CDL) restraints added in 1.7 seconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2040 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 6 sheets defined 72.7% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'B' and resid 136 through 145 removed outlier: 3.874A pdb=" N ARG B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N SER B 145 " --> pdb=" O LEU B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 167 removed outlier: 4.508A pdb=" N ALA B 154 " --> pdb=" O PRO B 150 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLY B 165 " --> pdb=" O LEU B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 181 Processing helix chain 'B' and resid 185 through 234 removed outlier: 3.749A pdb=" N SER B 191 " --> pdb=" O HIS B 187 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N PHE B 214 " --> pdb=" O ARG B 210 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG B 226 " --> pdb=" O ASN B 222 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N GLU B 227 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 244 removed outlier: 3.868A pdb=" N PHE B 241 " --> pdb=" O ASP B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 255 Processing helix chain 'B' and resid 255 through 260 removed outlier: 4.067A pdb=" N LEU B 259 " --> pdb=" O SER B 255 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N MET B 260 " --> pdb=" O ASP B 256 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 255 through 260' Processing helix chain 'B' and resid 266 through 289 Processing helix chain 'B' and resid 289 through 338 removed outlier: 3.851A pdb=" N LEU B 294 " --> pdb=" O PRO B 290 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N LEU B 295 " --> pdb=" O ARG B 291 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N SER B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Proline residue: B 301 - end of helix removed outlier: 3.898A pdb=" N GLN B 315 " --> pdb=" O ASN B 311 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 338 " --> pdb=" O GLU B 334 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 344 removed outlier: 3.572A pdb=" N VAL B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 402 removed outlier: 3.672A pdb=" N GLU B 351 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 385 " --> pdb=" O ARG B 381 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N LEU B 390 " --> pdb=" O GLY B 386 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER B 393 " --> pdb=" O MET B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 405 through 448 removed outlier: 4.048A pdb=" N GLU B 417 " --> pdb=" O MET B 413 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER B 418 " --> pdb=" O ILE B 414 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N SER B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TYR B 430 " --> pdb=" O LEU B 426 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLY B 431 " --> pdb=" O VAL B 427 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N ASP B 432 " --> pdb=" O TYR B 428 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N GLU B 441 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LYS B 442 " --> pdb=" O GLY B 438 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL B 443 " --> pdb=" O ALA B 439 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N TYR B 446 " --> pdb=" O LYS B 442 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 508 Processing helix chain 'B' and resid 509 through 517 removed outlier: 3.966A pdb=" N ALA B 513 " --> pdb=" O LYS B 509 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN B 517 " --> pdb=" O ALA B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 537 No H-bonds generated for 'chain 'B' and resid 535 through 537' Processing helix chain 'B' and resid 538 through 543 removed outlier: 3.699A pdb=" N HIS B 543 " --> pdb=" O HIS B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 565 removed outlier: 3.822A pdb=" N ALA B 565 " --> pdb=" O ARG B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 Processing helix chain 'B' and resid 585 through 590 removed outlier: 3.619A pdb=" N GLN B 590 " --> pdb=" O ASP B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 597 Processing helix chain 'B' and resid 601 through 605 Processing helix chain 'B' and resid 608 through 622 removed outlier: 3.569A pdb=" N ARG B 614 " --> pdb=" O GLY B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 636 removed outlier: 3.902A pdb=" N ALA B 636 " --> pdb=" O ALA B 633 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 633 through 636' Processing helix chain 'B' and resid 638 through 647 removed outlier: 3.579A pdb=" N LEU B 645 " --> pdb=" O CYS B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 653 removed outlier: 4.163A pdb=" N ASP B 653 " --> pdb=" O ASN B 649 " (cutoff:3.500A) Processing helix chain 'B' and resid 662 through 668 removed outlier: 4.161A pdb=" N THR B 665 " --> pdb=" O ARG B 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 182 removed outlier: 4.249A pdb=" N GLY A 181 " --> pdb=" O GLY A 178 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N SER A 182 " --> pdb=" O CYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 202 removed outlier: 3.653A pdb=" N LEU A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N MET A 202 " --> pdb=" O SER A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 218 removed outlier: 3.525A pdb=" N PHE A 206 " --> pdb=" O MET A 202 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 269 removed outlier: 4.428A pdb=" N ARG A 226 " --> pdb=" O ASP A 222 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N MET A 231 " --> pdb=" O ASN A 227 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 235 " --> pdb=" O MET A 231 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 248 " --> pdb=" O VAL A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 324 removed outlier: 4.147A pdb=" N THR A 292 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP A 297 " --> pdb=" O SER A 293 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER A 304 " --> pdb=" O SER A 300 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP A 322 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER A 324 " --> pdb=" O MET A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 373 removed outlier: 3.560A pdb=" N THR A 328 " --> pdb=" O SER A 324 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET A 329 " --> pdb=" O VAL A 325 " (cutoff:3.500A) Proline residue: A 336 - end of helix Proline residue: A 342 - end of helix removed outlier: 3.797A pdb=" N TRP A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 354 " --> pdb=" O GLN A 350 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA A 367 " --> pdb=" O SER A 363 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 373 " --> pdb=" O GLU A 369 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 381 Processing helix chain 'A' and resid 382 through 436 removed outlier: 3.740A pdb=" N ALA A 387 " --> pdb=" O GLU A 383 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS A 393 " --> pdb=" O LYS A 389 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU A 396 " --> pdb=" O GLU A 392 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ILE A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N LEU A 400 " --> pdb=" O GLU A 396 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N LYS A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N VAL A 406 " --> pdb=" O GLN A 402 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA A 407 " --> pdb=" O LYS A 403 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 409 " --> pdb=" O ALA A 405 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N VAL A 410 " --> pdb=" O VAL A 406 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A 422 " --> pdb=" O SER A 418 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 476 removed outlier: 3.556A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN A 456 " --> pdb=" O MET A 452 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N TYR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) Proline residue: A 466 - end of helix removed outlier: 3.636A pdb=" N GLU A 476 " --> pdb=" O VAL A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 483 removed outlier: 4.260A pdb=" N TYR A 481 " --> pdb=" O LYS A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 517 No H-bonds generated for 'chain 'A' and resid 515 through 517' Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 568 through 572 removed outlier: 3.871A pdb=" N TYR A 572 " --> pdb=" O LEU A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 581 removed outlier: 3.693A pdb=" N VAL A 581 " --> pdb=" O LEU A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 619 Processing helix chain 'A' and resid 621 through 626 Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 637 through 641 Processing helix chain 'A' and resid 644 through 660 removed outlier: 4.169A pdb=" N ALA A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 672 removed outlier: 3.510A pdb=" N ALA A 672 " --> pdb=" O ALA A 669 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 669 through 672' Processing helix chain 'A' and resid 674 through 688 Processing helix chain 'A' and resid 689 through 694 Processing helix chain 'A' and resid 702 through 709 Processing helix chain 'A' and resid 725 through 732 Processing helix chain 'A' and resid 734 through 739 Processing sheet with id=AA1, first strand: chain 'B' and resid 486 through 489 removed outlier: 6.233A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 486 through 489 removed outlier: 6.233A pdb=" N LYS B 487 " --> pdb=" O PHE B 475 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N PHE B 475 " --> pdb=" O LYS B 487 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLN B 471 " --> pdb=" O GLN B 526 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLN B 526 " --> pdb=" O GLN B 471 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N VAL B 473 " --> pdb=" O GLY B 524 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLY B 524 " --> pdb=" O VAL B 473 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 546 through 549 removed outlier: 6.656A pdb=" N VAL B 498 " --> pdb=" O GLN B 671 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N LEU B 673 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA B 500 " --> pdb=" O LEU B 673 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N LEU B 675 " --> pdb=" O ALA B 500 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N VAL B 502 " --> pdb=" O LEU B 675 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 558 through 559 removed outlier: 3.551A pdb=" N GLY B 558 " --> pdb=" O VAL B 600 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 519 through 524 removed outlier: 5.251A pdb=" N GLN A 522 " --> pdb=" O PHE A 510 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N PHE A 510 " --> pdb=" O GLN A 522 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N VAL A 508 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N GLY A 559 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 582 through 584 removed outlier: 3.658A pdb=" N ILE A 665 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ASP A 667 " --> pdb=" O VAL A 584 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 664 " --> pdb=" O LEU A 697 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ILE A 699 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU A 666 " --> pdb=" O ILE A 699 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N VAL A 533 " --> pdb=" O HIS A 711 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N LEU A 713 " --> pdb=" O VAL A 533 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA A 535 " --> pdb=" O LEU A 713 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N LEU A 715 " --> pdb=" O ALA A 535 " (cutoff:3.500A) removed outlier: 5.708A pdb=" N GLU A 716 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ILE A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) 553 hydrogen bonds defined for protein. 1605 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: 2.59 Time building geometry restraints manager: 3.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2659 1.34 - 1.46: 1728 1.46 - 1.58: 3508 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 7950 Sorted by residual: bond pdb=" CA ILE B 169 " pdb=" CB ILE B 169 " ideal model delta sigma weight residual 1.534 1.545 -0.010 6.80e-03 2.16e+04 2.38e+00 bond pdb=" CB GLU B 166 " pdb=" CG GLU B 166 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.54e+00 bond pdb=" CA ILE B 169 " pdb=" C ILE B 169 " ideal model delta sigma weight residual 1.520 1.530 -0.010 8.80e-03 1.29e+04 1.35e+00 bond pdb=" CA ILE A 665 " pdb=" CB ILE A 665 " ideal model delta sigma weight residual 1.551 1.540 0.011 1.08e-02 8.57e+03 1.05e+00 bond pdb=" C LYS A 660 " pdb=" O LYS A 660 " ideal model delta sigma weight residual 1.235 1.230 0.005 4.70e-03 4.53e+04 9.37e-01 ... (remaining 7945 not shown) Histogram of bond angle deviations from ideal: 99.06 - 106.05: 176 106.05 - 113.03: 4349 113.03 - 120.02: 2615 120.02 - 127.00: 3620 127.00 - 133.99: 69 Bond angle restraints: 10829 Sorted by residual: angle pdb=" CA GLU B 166 " pdb=" CB GLU B 166 " pdb=" CG GLU B 166 " ideal model delta sigma weight residual 114.10 121.34 -7.24 2.00e+00 2.50e-01 1.31e+01 angle pdb=" CB GLU B 166 " pdb=" CG GLU B 166 " pdb=" CD GLU B 166 " ideal model delta sigma weight residual 112.60 117.94 -5.34 1.70e+00 3.46e-01 9.88e+00 angle pdb=" N TYR A 692 " pdb=" CA TYR A 692 " pdb=" C TYR A 692 " ideal model delta sigma weight residual 114.04 110.17 3.87 1.24e+00 6.50e-01 9.72e+00 angle pdb=" N VAL A 520 " pdb=" CA VAL A 520 " pdb=" C VAL A 520 " ideal model delta sigma weight residual 113.20 110.34 2.86 9.60e-01 1.09e+00 8.86e+00 angle pdb=" N ILE B 169 " pdb=" CA ILE B 169 " pdb=" CB ILE B 169 " ideal model delta sigma weight residual 110.50 112.20 -1.70 6.30e-01 2.52e+00 7.29e+00 ... (remaining 10824 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4339 18.00 - 36.00: 313 36.00 - 54.00: 78 54.00 - 71.99: 7 71.99 - 89.99: 5 Dihedral angle restraints: 4742 sinusoidal: 1574 harmonic: 3168 Sorted by residual: dihedral pdb=" CA VAL B 387 " pdb=" C VAL B 387 " pdb=" N GLN B 388 " pdb=" CA GLN B 388 " ideal model delta harmonic sigma weight residual -180.00 -164.23 -15.77 0 5.00e+00 4.00e-02 9.95e+00 dihedral pdb=" CA ASN B 267 " pdb=" CB ASN B 267 " pdb=" CG ASN B 267 " pdb=" OD1 ASN B 267 " ideal model delta sinusoidal sigma weight residual 120.00 -177.32 -62.68 2 2.00e+01 2.50e-03 9.47e+00 dihedral pdb=" CA ARG B 561 " pdb=" CB ARG B 561 " pdb=" CG ARG B 561 " pdb=" CD ARG B 561 " ideal model delta sinusoidal sigma weight residual 60.00 117.76 -57.76 3 1.50e+01 4.44e-03 9.45e+00 ... (remaining 4739 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1010 0.042 - 0.084: 231 0.084 - 0.126: 51 0.126 - 0.167: 1 0.167 - 0.209: 2 Chirality restraints: 1295 Sorted by residual: chirality pdb=" CG LEU A 211 " pdb=" CB LEU A 211 " pdb=" CD1 LEU A 211 " pdb=" CD2 LEU A 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.72e-01 chirality pdb=" CG LEU B 295 " pdb=" CB LEU B 295 " pdb=" CD1 LEU B 295 " pdb=" CD2 LEU B 295 " both_signs ideal model delta sigma weight residual False -2.59 -2.45 -0.14 2.00e-01 2.50e+01 4.93e-01 ... (remaining 1292 not shown) Planarity restraints: 1415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG B 146 " -0.030 5.00e-02 4.00e+02 4.49e-02 3.22e+00 pdb=" N PRO B 147 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO B 147 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 147 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 204 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO A 205 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 339 " 0.008 2.00e-02 2.50e+03 1.17e-02 2.38e+00 pdb=" CG PHE A 339 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 339 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 339 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 PHE A 339 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 339 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 339 " -0.000 2.00e-02 2.50e+03 ... (remaining 1412 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2144 2.80 - 3.33: 8273 3.33 - 3.85: 12472 3.85 - 4.38: 13803 4.38 - 4.90: 23172 Nonbonded interactions: 59864 Sorted by model distance: nonbonded pdb=" O THR A 289 " pdb=" OG SER A 293 " model vdw 2.275 2.440 nonbonded pdb=" OH TYR A 249 " pdb=" O SER A 300 " model vdw 2.287 2.440 nonbonded pdb=" N GLU B 417 " pdb=" OE1 GLU B 417 " model vdw 2.302 2.520 nonbonded pdb=" O MET A 452 " pdb=" OG1 THR A 455 " model vdw 2.305 2.440 nonbonded pdb=" O LEU B 253 " pdb=" OG1 THR B 257 " model vdw 2.318 2.440 ... (remaining 59859 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 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: 4.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.320 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 26.920 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 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 : 0.002 0.037 7950 Z= 0.140 Angle : 0.600 8.583 10829 Z= 0.326 Chirality : 0.037 0.209 1295 Planarity : 0.003 0.045 1415 Dihedral : 13.692 89.993 2702 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.28 % Allowed : 12.94 % Favored : 86.78 % 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: 0.48 (0.26), residues: 1095 helix: 0.58 (0.20), residues: 698 sheet: -0.35 (0.73), residues: 66 loop : 0.20 (0.38), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 413 HIS 0.002 0.001 HIS B 543 PHE 0.027 0.001 PHE A 339 TYR 0.010 0.001 TYR B 376 ARG 0.004 0.000 ARG A 378 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 115 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: B 166 GLU cc_start: 0.8011 (tm-30) cc_final: 0.7674 (tt0) REVERT: B 254 SER cc_start: 0.9012 (t) cc_final: 0.8761 (p) REVERT: B 260 MET cc_start: 0.8357 (mmm) cc_final: 0.8135 (mmp) REVERT: B 366 TYR cc_start: 0.8523 (m-80) cc_final: 0.8272 (m-10) REVERT: B 467 VAL cc_start: 0.8277 (t) cc_final: 0.7924 (p) REVERT: A 189 LEU cc_start: 0.8072 (mm) cc_final: 0.7798 (tp) REVERT: A 191 LEU cc_start: 0.8771 (tt) cc_final: 0.7843 (mm) outliers start: 2 outliers final: 0 residues processed: 116 average time/residue: 0.1944 time to fit residues: 30.8940 Evaluate side-chains 89 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.0370 chunk 82 optimal weight: 0.0370 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 33 optimal weight: 0.5980 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 3.9990 chunk 98 optimal weight: 9.9990 overall best weight: 0.5136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.1650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7950 Z= 0.192 Angle : 0.607 10.370 10829 Z= 0.310 Chirality : 0.041 0.213 1295 Planarity : 0.004 0.044 1415 Dihedral : 3.762 23.565 1174 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.69 % Allowed : 13.92 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.26), residues: 1095 helix: 1.07 (0.19), residues: 700 sheet: -0.27 (0.68), residues: 72 loop : 0.06 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 413 HIS 0.003 0.001 HIS B 299 PHE 0.012 0.001 PHE B 214 TYR 0.015 0.001 TYR A 349 ARG 0.007 0.000 ARG A 391 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.904 Fit side-chains REVERT: B 166 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7593 (tt0) REVERT: B 385 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8336 (tt) REVERT: B 389 MET cc_start: 0.7751 (tpt) cc_final: 0.7350 (tpt) REVERT: B 391 MET cc_start: 0.8629 (tpp) cc_final: 0.8418 (tpp) REVERT: B 467 VAL cc_start: 0.8644 (t) cc_final: 0.8258 (p) REVERT: A 189 LEU cc_start: 0.8146 (mm) cc_final: 0.7788 (tp) REVERT: A 459 GLU cc_start: 0.8714 (tm-30) cc_final: 0.8440 (pp20) outliers start: 12 outliers final: 7 residues processed: 108 average time/residue: 0.1515 time to fit residues: 24.4207 Evaluate side-chains 91 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 225 ILE Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain A residue 194 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 chunk 27 optimal weight: 0.0020 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 50.0000 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 0.2980 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS ** B 667 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7950 Z= 0.198 Angle : 0.562 9.991 10829 Z= 0.285 Chirality : 0.041 0.205 1295 Planarity : 0.004 0.036 1415 Dihedral : 3.627 17.829 1174 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.66 % Allowed : 14.35 % Favored : 82.00 % 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: 1.16 (0.26), residues: 1095 helix: 1.27 (0.19), residues: 700 sheet: -0.30 (0.68), residues: 72 loop : 0.11 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 413 HIS 0.004 0.001 HIS B 299 PHE 0.015 0.001 PHE A 479 TYR 0.019 0.001 TYR A 349 ARG 0.006 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 89 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: B 166 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7659 (tt0) REVERT: B 260 MET cc_start: 0.8484 (tpp) cc_final: 0.8212 (mtm) REVERT: B 385 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8237 (tt) REVERT: B 390 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8336 (tp) REVERT: B 467 VAL cc_start: 0.8707 (t) cc_final: 0.8346 (p) REVERT: A 191 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.7618 (mt) REVERT: A 213 ASP cc_start: 0.8730 (m-30) cc_final: 0.8420 (m-30) outliers start: 26 outliers final: 13 residues processed: 108 average time/residue: 0.1428 time to fit residues: 23.8035 Evaluate side-chains 97 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 307 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 105 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 chunk 87 optimal weight: 30.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS A 261 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7950 Z= 0.191 Angle : 0.551 10.384 10829 Z= 0.277 Chirality : 0.040 0.208 1295 Planarity : 0.003 0.036 1415 Dihedral : 3.555 17.334 1174 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.66 % Allowed : 17.30 % Favored : 79.04 % 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: 1.26 (0.26), residues: 1095 helix: 1.41 (0.19), residues: 710 sheet: -0.29 (0.67), residues: 71 loop : -0.05 (0.39), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.004 0.001 HIS B 299 PHE 0.010 0.001 PHE B 214 TYR 0.011 0.001 TYR A 309 ARG 0.003 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 84 time to evaluate : 0.940 Fit side-chains revert: symmetry clash REVERT: B 218 MET cc_start: 0.8078 (tmm) cc_final: 0.7867 (tmm) REVERT: B 385 LEU cc_start: 0.8593 (OUTLIER) cc_final: 0.8222 (tt) REVERT: B 391 MET cc_start: 0.8604 (tpp) cc_final: 0.8387 (tpp) REVERT: B 467 VAL cc_start: 0.8724 (t) cc_final: 0.8384 (p) REVERT: B 680 LEU cc_start: 0.6812 (OUTLIER) cc_final: 0.6289 (pt) REVERT: A 191 LEU cc_start: 0.8568 (OUTLIER) cc_final: 0.7620 (mt) REVERT: A 213 ASP cc_start: 0.8683 (m-30) cc_final: 0.8367 (m-30) outliers start: 26 outliers final: 19 residues processed: 103 average time/residue: 0.1381 time to fit residues: 22.4370 Evaluate side-chains 104 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 82 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 89 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS B 406 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 7950 Z= 0.235 Angle : 0.562 10.277 10829 Z= 0.283 Chirality : 0.041 0.217 1295 Planarity : 0.004 0.037 1415 Dihedral : 3.562 16.741 1174 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.08 % Allowed : 18.14 % Favored : 77.78 % 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: 1095 helix: 1.40 (0.19), residues: 710 sheet: -0.22 (0.67), residues: 69 loop : -0.12 (0.38), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.005 0.001 HIS B 299 PHE 0.010 0.001 PHE B 588 TYR 0.011 0.001 TYR A 349 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 85 time to evaluate : 0.846 Fit side-chains REVERT: B 166 GLU cc_start: 0.8121 (tm-30) cc_final: 0.7671 (tt0) REVERT: B 218 MET cc_start: 0.8080 (tmm) cc_final: 0.7831 (tmm) REVERT: B 260 MET cc_start: 0.8400 (tpp) cc_final: 0.8103 (mtp) REVERT: B 385 LEU cc_start: 0.8578 (OUTLIER) cc_final: 0.8205 (tt) REVERT: B 413 MET cc_start: 0.8399 (tpp) cc_final: 0.7734 (tpp) REVERT: B 467 VAL cc_start: 0.8847 (t) cc_final: 0.8461 (p) REVERT: B 493 LEU cc_start: 0.6442 (OUTLIER) cc_final: 0.6187 (mt) REVERT: A 191 LEU cc_start: 0.8592 (OUTLIER) cc_final: 0.7653 (mt) REVERT: A 213 ASP cc_start: 0.8617 (m-30) cc_final: 0.8337 (m-30) outliers start: 29 outliers final: 23 residues processed: 107 average time/residue: 0.1304 time to fit residues: 21.7787 Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 83 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 285 MET Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 61 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 chunk 48 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 55 optimal weight: 0.9980 chunk 101 optimal weight: 0.0040 overall best weight: 0.5530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7950 Z= 0.164 Angle : 0.548 10.685 10829 Z= 0.269 Chirality : 0.039 0.207 1295 Planarity : 0.003 0.036 1415 Dihedral : 3.474 16.685 1174 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.94 % Allowed : 18.71 % Favored : 77.36 % 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: 1.38 (0.26), residues: 1095 helix: 1.56 (0.19), residues: 710 sheet: -0.37 (0.65), residues: 74 loop : -0.14 (0.39), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.004 0.001 HIS B 299 PHE 0.043 0.002 PHE A 447 TYR 0.010 0.001 TYR A 309 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 91 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: B 260 MET cc_start: 0.8332 (tpp) cc_final: 0.8091 (mtp) REVERT: B 385 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8139 (tp) REVERT: B 389 MET cc_start: 0.7837 (tpt) cc_final: 0.7374 (tpt) REVERT: B 413 MET cc_start: 0.8341 (tpp) cc_final: 0.7982 (tpp) REVERT: B 424 GLN cc_start: 0.8871 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 467 VAL cc_start: 0.8700 (t) cc_final: 0.8383 (p) REVERT: B 493 LEU cc_start: 0.6531 (OUTLIER) cc_final: 0.6315 (mt) REVERT: B 680 LEU cc_start: 0.6798 (OUTLIER) cc_final: 0.6406 (pt) REVERT: A 191 LEU cc_start: 0.8558 (OUTLIER) cc_final: 0.7644 (mt) REVERT: A 213 ASP cc_start: 0.8541 (m-30) cc_final: 0.8233 (m-30) outliers start: 28 outliers final: 15 residues processed: 113 average time/residue: 0.1354 time to fit residues: 23.3655 Evaluate side-chains 103 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 84 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 307 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 88 optimal weight: 8.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 41 optimal weight: 7.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.2802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 7950 Z= 0.198 Angle : 0.569 10.281 10829 Z= 0.279 Chirality : 0.040 0.232 1295 Planarity : 0.003 0.036 1415 Dihedral : 3.460 16.961 1174 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 4.22 % Allowed : 18.99 % Favored : 76.79 % 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: 1.35 (0.26), residues: 1095 helix: 1.55 (0.19), residues: 712 sheet: -0.38 (0.65), residues: 74 loop : -0.19 (0.39), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.005 0.001 HIS B 299 PHE 0.033 0.001 PHE A 447 TYR 0.010 0.001 TYR B 376 ARG 0.005 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 83 time to evaluate : 0.906 Fit side-chains REVERT: B 166 GLU cc_start: 0.8149 (tm-30) cc_final: 0.7657 (tt0) REVERT: B 385 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.8179 (tp) REVERT: B 389 MET cc_start: 0.7797 (tpt) cc_final: 0.7376 (tpt) REVERT: B 424 GLN cc_start: 0.8829 (tm-30) cc_final: 0.8492 (tm-30) REVERT: B 467 VAL cc_start: 0.8705 (t) cc_final: 0.8394 (p) REVERT: B 493 LEU cc_start: 0.6606 (OUTLIER) cc_final: 0.6369 (mt) REVERT: B 680 LEU cc_start: 0.6700 (OUTLIER) cc_final: 0.6303 (pt) REVERT: A 191 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.7636 (mt) REVERT: A 213 ASP cc_start: 0.8554 (m-30) cc_final: 0.8278 (m-30) outliers start: 30 outliers final: 21 residues processed: 107 average time/residue: 0.1400 time to fit residues: 23.0086 Evaluate side-chains 108 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 83 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 161 LEU Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 366 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 95 optimal weight: 0.2980 chunk 100 optimal weight: 4.9990 chunk 91 optimal weight: 20.0000 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7950 Z= 0.189 Angle : 0.573 11.051 10829 Z= 0.279 Chirality : 0.040 0.216 1295 Planarity : 0.003 0.034 1415 Dihedral : 3.449 17.061 1174 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.80 % Allowed : 19.83 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.26), residues: 1095 helix: 1.59 (0.19), residues: 711 sheet: -0.37 (0.65), residues: 74 loop : -0.17 (0.39), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 308 HIS 0.005 0.001 HIS B 299 PHE 0.028 0.001 PHE A 447 TYR 0.011 0.001 TYR B 366 ARG 0.007 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 82 time to evaluate : 0.926 Fit side-chains REVERT: B 166 GLU cc_start: 0.8081 (tm-30) cc_final: 0.7632 (tt0) REVERT: B 385 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8176 (tt) REVERT: B 389 MET cc_start: 0.7697 (tpt) cc_final: 0.7256 (tpt) REVERT: B 424 GLN cc_start: 0.8804 (tm-30) cc_final: 0.8593 (tm-30) REVERT: B 467 VAL cc_start: 0.8721 (t) cc_final: 0.8417 (p) REVERT: B 493 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6371 (mt) REVERT: B 680 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6377 (pt) REVERT: A 191 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7643 (mt) REVERT: A 213 ASP cc_start: 0.8553 (m-30) cc_final: 0.8257 (m-30) outliers start: 27 outliers final: 20 residues processed: 105 average time/residue: 0.1389 time to fit residues: 22.3047 Evaluate side-chains 106 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 453 LEU Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 76 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 64 optimal weight: 9.9990 chunk 103 optimal weight: 10.0000 chunk 63 optimal weight: 2.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS A 469 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7950 Z= 0.354 Angle : 0.692 10.759 10829 Z= 0.344 Chirality : 0.044 0.227 1295 Planarity : 0.004 0.040 1415 Dihedral : 3.791 17.412 1174 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 4.64 % Allowed : 19.55 % Favored : 75.81 % 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 (0.26), residues: 1095 helix: 1.24 (0.19), residues: 704 sheet: -0.52 (0.66), residues: 69 loop : -0.16 (0.38), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 413 HIS 0.005 0.001 HIS B 299 PHE 0.027 0.002 PHE A 447 TYR 0.014 0.002 TYR B 376 ARG 0.007 0.000 ARG B 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 82 time to evaluate : 0.917 Fit side-chains REVERT: B 166 GLU cc_start: 0.8084 (tm-30) cc_final: 0.7643 (tt0) REVERT: B 319 ARG cc_start: 0.8471 (mmm160) cc_final: 0.7998 (mmm160) REVERT: B 385 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8266 (tp) REVERT: B 389 MET cc_start: 0.7822 (tpt) cc_final: 0.7341 (tpt) REVERT: B 424 GLN cc_start: 0.8802 (tm-30) cc_final: 0.8573 (tm-30) REVERT: B 467 VAL cc_start: 0.8984 (t) cc_final: 0.8619 (p) REVERT: B 493 LEU cc_start: 0.6583 (OUTLIER) cc_final: 0.6317 (mt) REVERT: A 191 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.7539 (mt) outliers start: 33 outliers final: 26 residues processed: 109 average time/residue: 0.1451 time to fit residues: 24.1187 Evaluate side-chains 110 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 81 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 40.0000 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 350 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7950 Z= 0.205 Angle : 0.621 11.814 10829 Z= 0.299 Chirality : 0.040 0.212 1295 Planarity : 0.004 0.036 1415 Dihedral : 3.612 17.228 1174 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.94 % Allowed : 20.39 % Favored : 75.67 % 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: 1095 helix: 1.46 (0.20), residues: 705 sheet: -0.35 (0.65), residues: 72 loop : -0.23 (0.37), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 308 HIS 0.005 0.001 HIS B 299 PHE 0.029 0.001 PHE A 447 TYR 0.017 0.001 TYR A 465 ARG 0.008 0.000 ARG B 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 0.857 Fit side-chains REVERT: B 166 GLU cc_start: 0.8042 (tm-30) cc_final: 0.7707 (tt0) REVERT: B 319 ARG cc_start: 0.8457 (mmm160) cc_final: 0.7994 (mmm160) REVERT: B 385 LEU cc_start: 0.8565 (OUTLIER) cc_final: 0.8207 (tp) REVERT: B 389 MET cc_start: 0.7727 (tpt) cc_final: 0.7259 (tpt) REVERT: B 467 VAL cc_start: 0.8802 (t) cc_final: 0.8515 (p) REVERT: B 493 LEU cc_start: 0.6475 (OUTLIER) cc_final: 0.6259 (mt) REVERT: B 680 LEU cc_start: 0.6746 (OUTLIER) cc_final: 0.6358 (pt) REVERT: A 191 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7615 (mt) REVERT: A 213 ASP cc_start: 0.8590 (m-30) cc_final: 0.8299 (m-30) outliers start: 28 outliers final: 24 residues processed: 104 average time/residue: 0.1331 time to fit residues: 21.3439 Evaluate side-chains 109 residues out of total 939 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 81 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 136 VAL Chi-restraints excluded: chain B residue 177 ILE Chi-restraints excluded: chain B residue 199 PHE Chi-restraints excluded: chain B residue 205 LEU Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 246 THR Chi-restraints excluded: chain B residue 314 HIS Chi-restraints excluded: chain B residue 385 LEU Chi-restraints excluded: chain B residue 423 VAL Chi-restraints excluded: chain B residue 427 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 443 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 501 LEU Chi-restraints excluded: chain B residue 560 VAL Chi-restraints excluded: chain B residue 628 LEU Chi-restraints excluded: chain B residue 656 VAL Chi-restraints excluded: chain B residue 674 VAL Chi-restraints excluded: chain B residue 680 LEU Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 421 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 0.0870 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 86 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- 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 = 0.3969 r_free = 0.3969 target = 0.124828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.097370 restraints weight = 18537.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.096079 restraints weight = 12812.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.097596 restraints weight = 9802.531| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7950 Z= 0.165 Angle : 0.603 11.132 10829 Z= 0.291 Chirality : 0.039 0.210 1295 Planarity : 0.003 0.033 1415 Dihedral : 3.437 16.819 1174 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.52 % Allowed : 21.10 % Favored : 75.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.26), residues: 1095 helix: 1.62 (0.20), residues: 712 sheet: -0.23 (0.66), residues: 72 loop : -0.23 (0.38), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 308 HIS 0.005 0.001 HIS B 299 PHE 0.027 0.001 PHE A 447 TYR 0.013 0.001 TYR A 465 ARG 0.007 0.000 ARG B 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1720.65 seconds wall clock time: 31 minutes 30.53 seconds (1890.53 seconds total)