Starting phenix.real_space_refine on Mon May 12 20:25:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k7c_36938/05_2025/8k7c_36938.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k7c_36938/05_2025/8k7c_36938.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/cci-nas-00/data/ceres_data/8k7c_36938/05_2025/8k7c_36938.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k7c_36938/05_2025/8k7c_36938.map" model { file = "/net/cci-nas-00/data/ceres_data/8k7c_36938/05_2025/8k7c_36938.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k7c_36938/05_2025/8k7c_36938.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= 0.004 sd= 0.041 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: 7 Type Number sf(0) Gaussians V 2 8.30 5 P 4 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 5925 2.51 5 N 1606 2.21 5 O 1698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9271 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4618 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 13, 'TRANS': 573} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 18 Chain: "B" Number of atoms: 4587 Number of conformers: 1 Conformer: "" Number of residues, atoms: 587, 4587 Classifications: {'peptide': 587} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 13, 'TRANS': 573} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 77 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'TRP:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 41 Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'VO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.65, per 1000 atoms: 0.61 Number of scatterers: 9271 At special positions: 0 Unit cell: (84.249, 84.249, 142.117, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) V 2 22.97 S 34 16.00 P 4 15.00 Mg 2 11.99 O 1698 8.00 N 1606 7.00 C 5925 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 - 3.00 Amino acid : True - 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: 2.38 Conformation dependent library (CDL) restraints added in 1.0 seconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 8 sheets defined 69.4% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 240 through 254 removed outlier: 3.977A pdb=" N ARG A 244 " --> pdb=" O ARG A 240 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLY A 251 " --> pdb=" O ARG A 247 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N TYR A 252 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N TRP A 254 " --> pdb=" O SER A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 258 through 296 removed outlier: 3.695A pdb=" N VAL A 264 " --> pdb=" O ALA A 260 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N VAL A 265 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU A 266 " --> pdb=" O GLN A 262 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARG A 276 " --> pdb=" O MET A 272 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA A 277 " --> pdb=" O GLY A 273 " (cutoff:3.500A) Proline residue: A 283 - end of helix removed outlier: 3.544A pdb=" N LYS A 296 " --> pdb=" O LEU A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 317 removed outlier: 3.510A pdb=" N LEU A 302 " --> pdb=" O PRO A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 322 removed outlier: 4.411A pdb=" N GLY A 321 " --> pdb=" O GLY A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.735A pdb=" N ARG A 330 " --> pdb=" O VAL A 326 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N THR A 331 " --> pdb=" O SER A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 354 removed outlier: 3.539A pdb=" N VAL A 345 " --> pdb=" O THR A 341 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU A 346 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N SER A 351 " --> pdb=" O LEU A 347 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N HIS A 354 " --> pdb=" O PHE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 3.557A pdb=" N HIS A 361 " --> pdb=" O SER A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 388 removed outlier: 3.539A pdb=" N VAL A 369 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 373 " --> pdb=" O VAL A 369 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASP A 374 " --> pdb=" O LEU A 370 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A 378 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER A 385 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 404 Processing helix chain 'A' and resid 412 through 432 removed outlier: 3.999A pdb=" N ILE A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 417 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL A 430 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N VAL A 431 " --> pdb=" O LEU A 427 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR A 432 " --> pdb=" O THR A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 459 removed outlier: 4.259A pdb=" N THR A 436 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ALA A 448 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N THR A 449 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N SER A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASN A 459 " --> pdb=" O ASP A 455 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 466 removed outlier: 3.677A pdb=" N VAL A 463 " --> pdb=" O ASN A 459 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR A 466 " --> pdb=" O THR A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 520 removed outlier: 3.770A pdb=" N GLU A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N TYR A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA A 492 " --> pdb=" O TRP A 488 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LEU A 497 " --> pdb=" O SER A 493 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 504 " --> pdb=" O THR A 500 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE A 505 " --> pdb=" O GLN A 501 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLY A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 568 removed outlier: 3.736A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N THR A 535 " --> pdb=" O VAL A 531 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 540 " --> pdb=" O TYR A 536 " (cutoff:3.500A) Proline residue: A 543 - end of helix removed outlier: 3.587A pdb=" N ARG A 552 " --> pdb=" O GLY A 548 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET A 553 " --> pdb=" O THR A 549 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASN A 563 " --> pdb=" O ILE A 559 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N MET A 564 " --> pdb=" O ASP A 560 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 565 " --> pdb=" O MET A 561 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASP A 566 " --> pdb=" O GLU A 562 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N LEU A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 637 removed outlier: 3.922A pdb=" N ILE A 632 " --> pdb=" O GLY A 628 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LEU A 633 " --> pdb=" O LYS A 629 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N PHE A 637 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 665 removed outlier: 3.714A pdb=" N LEU A 662 " --> pdb=" O THR A 658 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG A 663 " --> pdb=" O GLN A 659 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER A 664 " --> pdb=" O ALA A 660 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N HIS A 665 " --> pdb=" O SER A 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 658 through 665' Processing helix chain 'A' and resid 679 through 685 removed outlier: 3.716A pdb=" N ARG A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 688 No H-bonds generated for 'chain 'A' and resid 686 through 688' Processing helix chain 'A' and resid 694 through 703 removed outlier: 3.570A pdb=" N ALA A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 705 through 711 removed outlier: 4.095A pdb=" N ALA A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 718 Processing helix chain 'A' and resid 721 through 725 removed outlier: 3.606A pdb=" N LEU A 725 " --> pdb=" O GLU A 722 " (cutoff:3.500A) Processing helix chain 'A' and resid 730 through 744 removed outlier: 3.545A pdb=" N ARG A 734 " --> pdb=" O GLY A 730 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 740 " --> pdb=" O ALA A 736 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ILE A 741 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 772 removed outlier: 4.085A pdb=" N ARG A 763 " --> pdb=" O THR A 759 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 788 Processing helix chain 'A' and resid 807 through 813 Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'B' and resid 241 through 253 removed outlier: 3.828A pdb=" N ARG B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU B 248 " --> pdb=" O ARG B 244 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N TYR B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 295 removed outlier: 3.980A pdb=" N VAL B 264 " --> pdb=" O ALA B 260 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N VAL B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N LEU B 266 " --> pdb=" O GLN B 262 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 267 " --> pdb=" O LEU B 263 " (cutoff:3.500A) Proline residue: B 283 - end of helix removed outlier: 3.921A pdb=" N GLU B 295 " --> pdb=" O ASN B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 317 Processing helix chain 'B' and resid 318 through 322 removed outlier: 4.042A pdb=" N GLY B 321 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 333 removed outlier: 3.585A pdb=" N THR B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) Processing helix chain 'B' and resid 334 through 352 removed outlier: 3.531A pdb=" N GLU B 346 " --> pdb=" O SER B 342 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU B 348 " --> pdb=" O ARG B 344 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER B 351 " --> pdb=" O LEU B 347 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 363 removed outlier: 3.774A pdb=" N HIS B 361 " --> pdb=" O SER B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 390 removed outlier: 3.789A pdb=" N ALA B 373 " --> pdb=" O VAL B 369 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ASP B 374 " --> pdb=" O LEU B 370 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N THR B 381 " --> pdb=" O THR B 377 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 385 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 386 " --> pdb=" O GLY B 382 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 404 Processing helix chain 'B' and resid 412 through 437 removed outlier: 3.537A pdb=" N ILE B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL B 430 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N THR B 432 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N TRP B 434 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ARG B 435 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 458 removed outlier: 3.536A pdb=" N ASN B 447 " --> pdb=" O ASN B 443 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA B 448 " --> pdb=" O THR B 444 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR B 449 " --> pdb=" O GLN B 445 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 460 through 465 Processing helix chain 'B' and resid 471 through 521 removed outlier: 3.577A pdb=" N GLU B 478 " --> pdb=" O GLU B 474 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR B 483 " --> pdb=" O ALA B 479 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N SER B 493 " --> pdb=" O LYS B 489 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N LEU B 494 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N VAL B 495 " --> pdb=" O SER B 491 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLN B 501 " --> pdb=" O LEU B 497 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ASN B 502 " --> pdb=" O ASN B 498 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 504 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE B 505 " --> pdb=" O GLN B 501 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 550 removed outlier: 3.944A pdb=" N THR B 535 " --> pdb=" O VAL B 531 " (cutoff:3.500A) Proline residue: B 543 - end of helix removed outlier: 4.262A pdb=" N PHE B 547 " --> pdb=" O PRO B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 570 removed outlier: 3.711A pdb=" N GLN B 555 " --> pdb=" O TYR B 551 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N ASP B 566 " --> pdb=" O GLU B 562 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU B 568 " --> pdb=" O MET B 564 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B 570 " --> pdb=" O ASP B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 637 removed outlier: 3.669A pdb=" N LEU B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N PHE B 637 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 658 through 665 removed outlier: 3.612A pdb=" N LEU B 662 " --> pdb=" O THR B 658 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N SER B 664 " --> pdb=" O ALA B 660 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N HIS B 665 " --> pdb=" O SER B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 686 removed outlier: 3.583A pdb=" N ARG B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 692 through 704 removed outlier: 3.505A pdb=" N GLU B 697 " --> pdb=" O ASN B 693 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLN B 701 " --> pdb=" O GLU B 697 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ALA B 702 " --> pdb=" O ALA B 698 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA B 703 " --> pdb=" O ALA B 699 " (cutoff:3.500A) Processing helix chain 'B' and resid 705 through 711 removed outlier: 3.802A pdb=" N MET B 710 " --> pdb=" O HIS B 706 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 711 " --> pdb=" O ASP B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 718 Processing helix chain 'B' and resid 721 through 725 removed outlier: 3.530A pdb=" N LEU B 725 " --> pdb=" O GLU B 722 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 744 removed outlier: 3.608A pdb=" N ARG B 734 " --> pdb=" O GLY B 730 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA B 736 " --> pdb=" O LYS B 732 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE B 741 " --> pdb=" O ILE B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 772 removed outlier: 3.618A pdb=" N GLU B 762 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG B 763 " --> pdb=" O THR B 759 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL B 772 " --> pdb=" O SER B 768 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 789 removed outlier: 3.541A pdb=" N THR B 787 " --> pdb=" O ARG B 784 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VAL B 788 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 813 removed outlier: 4.351A pdb=" N SER B 813 " --> pdb=" O GLU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing sheet with id=AA1, first strand: chain 'A' and resid 606 through 609 removed outlier: 6.343A pdb=" N VAL A 595 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 590 " --> pdb=" O VAL A 613 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 606 through 609 removed outlier: 6.343A pdb=" N VAL A 595 " --> pdb=" O ASP A 608 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N VAL A 595 " --> pdb=" O SER A 644 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N SER A 644 " --> pdb=" O VAL A 595 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 778 through 781 removed outlier: 3.520A pdb=" N LEU A 621 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR A 618 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 8.067A pdb=" N LEU A 795 " --> pdb=" O THR A 618 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA A 620 " --> pdb=" O LEU A 795 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 666 through 669 removed outlier: 3.646A pdb=" N VAL A 669 " --> pdb=" O LEU A 749 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 606 through 609 removed outlier: 3.525A pdb=" N PHE B 597 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 595 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE B 590 " --> pdb=" O VAL B 613 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 606 through 609 removed outlier: 3.525A pdb=" N PHE B 597 " --> pdb=" O LEU B 606 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N VAL B 595 " --> pdb=" O ASP B 608 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS B 646 " --> pdb=" O GLU B 593 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N VAL B 595 " --> pdb=" O SER B 644 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER B 644 " --> pdb=" O VAL B 595 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 778 through 781 removed outlier: 6.238A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N THR B 618 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LEU B 795 " --> pdb=" O THR B 618 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N ALA B 620 " --> pdb=" O LEU B 795 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE B 797 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL B 622 " --> pdb=" O ILE B 797 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ILE B 794 " --> pdb=" O ARG B 805 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N ARG B 805 " --> pdb=" O ILE B 794 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N VAL B 796 " --> pdb=" O VAL B 803 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 666 through 669 removed outlier: 3.951A pdb=" N VAL B 669 " --> pdb=" O LEU B 749 " (cutoff:3.500A) 476 hydrogen bonds defined for protein. 1380 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: 2.71 Time building geometry restraints manager: 2.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 3091 1.35 - 1.49: 2574 1.49 - 1.63: 3714 1.63 - 1.77: 1 1.77 - 1.91: 63 Bond restraints: 9443 Sorted by residual: bond pdb=" CA ALA B 753 " pdb=" C ALA B 753 " ideal model delta sigma weight residual 1.524 1.479 0.045 1.24e-02 6.50e+03 1.32e+01 bond pdb=" CA THR A 658 " pdb=" C THR A 658 " ideal model delta sigma weight residual 1.525 1.484 0.040 1.28e-02 6.10e+03 9.88e+00 bond pdb=" CA SER B 755 " pdb=" C SER B 755 " ideal model delta sigma weight residual 1.524 1.489 0.035 1.16e-02 7.43e+03 9.13e+00 bond pdb=" CA VAL A 574 " pdb=" CB VAL A 574 " ideal model delta sigma weight residual 1.539 1.507 0.032 1.20e-02 6.94e+03 7.33e+00 bond pdb=" CA MET A 564 " pdb=" C MET A 564 " ideal model delta sigma weight residual 1.524 1.489 0.034 1.29e-02 6.01e+03 7.07e+00 ... (remaining 9438 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 11864 1.66 - 3.32: 760 3.32 - 4.98: 151 4.98 - 6.64: 37 6.64 - 8.31: 7 Bond angle restraints: 12819 Sorted by residual: angle pdb=" N LEU A 248 " pdb=" CA LEU A 248 " pdb=" C LEU A 248 " ideal model delta sigma weight residual 111.07 105.15 5.92 1.07e+00 8.73e-01 3.06e+01 angle pdb=" N LYS A 524 " pdb=" CA LYS A 524 " pdb=" C LYS A 524 " ideal model delta sigma weight residual 114.64 108.25 6.39 1.52e+00 4.33e-01 1.77e+01 angle pdb=" N SER B 755 " pdb=" CA SER B 755 " pdb=" C SER B 755 " ideal model delta sigma weight residual 112.68 107.11 5.57 1.33e+00 5.65e-01 1.75e+01 angle pdb=" C LEU B 248 " pdb=" N LEU B 249 " pdb=" CA LEU B 249 " ideal model delta sigma weight residual 120.44 115.01 5.43 1.30e+00 5.92e-01 1.75e+01 angle pdb=" N ILE A 765 " pdb=" CA ILE A 765 " pdb=" C ILE A 765 " ideal model delta sigma weight residual 110.36 106.03 4.33 1.05e+00 9.07e-01 1.70e+01 ... (remaining 12814 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.86: 5265 23.86 - 47.71: 275 47.71 - 71.57: 18 71.57 - 95.42: 8 95.42 - 119.28: 1 Dihedral angle restraints: 5567 sinusoidal: 2191 harmonic: 3376 Sorted by residual: dihedral pdb=" O1B ADP B 901 " pdb=" O3A ADP B 901 " pdb=" PB ADP B 901 " pdb=" PA ADP B 901 " ideal model delta sinusoidal sigma weight residual -60.00 -179.28 119.28 1 2.00e+01 2.50e-03 3.57e+01 dihedral pdb=" CA ARG A 638 " pdb=" C ARG A 638 " pdb=" N PHE A 639 " pdb=" CA PHE A 639 " ideal model delta harmonic sigma weight residual 180.00 156.21 23.79 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLY A 319 " pdb=" C GLY A 319 " pdb=" N THR A 320 " pdb=" CA THR A 320 " ideal model delta harmonic sigma weight residual 180.00 -158.22 -21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 5564 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.111: 1440 0.111 - 0.222: 48 0.222 - 0.333: 0 0.333 - 0.444: 0 0.444 - 0.555: 1 Chirality restraints: 1489 Sorted by residual: chirality pdb=" V VO4 B 902 " pdb=" O1 VO4 B 902 " pdb=" O2 VO4 B 902 " pdb=" O4 VO4 B 902 " both_signs ideal model delta sigma weight residual True 5.36 5.92 -0.55 2.00e-01 2.50e+01 7.69e+00 chirality pdb=" CA PHE B 558 " pdb=" N PHE B 558 " pdb=" C PHE B 558 " pdb=" CB PHE B 558 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 8.24e-01 chirality pdb=" CB VAL B 463 " pdb=" CA VAL B 463 " pdb=" CG1 VAL B 463 " pdb=" CG2 VAL B 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.91e-01 ... (remaining 1486 not shown) Planarity restraints: 1615 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 744 " 0.073 5.00e-02 4.00e+02 1.10e-01 1.93e+01 pdb=" N PRO B 745 " -0.190 5.00e-02 4.00e+02 pdb=" CA PRO B 745 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO B 745 " 0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 542 " 0.046 5.00e-02 4.00e+02 7.00e-02 7.83e+00 pdb=" N PRO B 543 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO B 543 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 543 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 488 " -0.018 2.00e-02 2.50e+03 1.57e-02 6.18e+00 pdb=" CG TRP B 488 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 TRP B 488 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 488 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP B 488 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 488 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP B 488 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 488 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 488 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP B 488 " -0.004 2.00e-02 2.50e+03 ... (remaining 1612 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 44 2.45 - 3.06: 6973 3.06 - 3.67: 12987 3.67 - 4.29: 17709 4.29 - 4.90: 28144 Nonbonded interactions: 65857 Sorted by model distance: nonbonded pdb=" OG SER B 630 " pdb="MG MG B 903 " model vdw 1.837 2.170 nonbonded pdb=" OG SER A 630 " pdb="MG MG A 903 " model vdw 1.902 2.170 nonbonded pdb=" OE1 GLN A 671 " pdb="MG MG A 903 " model vdw 1.909 2.170 nonbonded pdb=" O3B ADP A 901 " pdb="MG MG A 903 " model vdw 2.074 2.170 nonbonded pdb=" OD1 ASP B 678 " pdb=" N THR B 679 " model vdw 2.074 3.120 ... (remaining 65852 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 240 through 244 or (resid 245 and (name N or name CA or na \ me C or name O or name CB )) or resid 246 or (resid 247 through 248 and (name N \ or name CA or name C or name O or name CB )) or resid 249 through 298 or (resid \ 299 and (name N or name CA or name C or name O or name CB )) or resid 300 throug \ h 301 or (resid 302 through 304 and (name N or name CA or name C or name O or na \ me CB )) or resid 305 through 514 or (resid 515 and (name N or name CA or name C \ or name O or name CB )) or resid 516 through 518 or (resid 519 and (name N or n \ ame CA or name C or name O or name CB )) or resid 520 through 826 or resid 901 t \ hrough 903)) selection = (chain 'B' and (resid 240 through 247 or (resid 248 and (name N or name CA or na \ me C or name O or name CB )) or resid 249 through 412 or (resid 413 and (name N \ or name CA or name C or name O or name CB )) or resid 414 through 826 or resid 9 \ 01 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.610 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: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.960 Find NCS groups from input model: 0.340 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 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 : 0.009 0.056 9443 Z= 0.447 Angle : 0.957 8.306 12819 Z= 0.555 Chirality : 0.051 0.555 1489 Planarity : 0.005 0.110 1615 Dihedral : 13.867 119.276 3407 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.80 % Favored : 91.20 % Rotamer: Outliers : 0.21 % Allowed : 1.33 % Favored : 98.46 % 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: -1.19 (0.24), residues: 1170 helix: -0.26 (0.20), residues: 670 sheet: -0.82 (0.58), residues: 78 loop : -1.49 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP B 488 HIS 0.010 0.002 HIS A 361 PHE 0.038 0.003 PHE A 558 TYR 0.031 0.003 TYR A 483 ARG 0.004 0.001 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.22579 ( 471) hydrogen bonds : angle 7.55571 ( 1380) covalent geometry : bond 0.00922 ( 9443) covalent geometry : angle 0.95709 (12819) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 151 time to evaluate : 1.048 Fit side-chains REVERT: A 246 LEU cc_start: 0.8388 (mm) cc_final: 0.7967 (mm) REVERT: A 754 THR cc_start: 0.7130 (p) cc_final: 0.6605 (p) REVERT: B 407 MET cc_start: 0.6652 (ppp) cc_final: 0.6366 (ppp) REVERT: B 547 PHE cc_start: 0.8069 (t80) cc_final: 0.7597 (t80) REVERT: B 587 LYS cc_start: 0.8859 (mppt) cc_final: 0.8583 (mppt) REVERT: B 801 CYS cc_start: 0.9131 (p) cc_final: 0.8921 (p) outliers start: 2 outliers final: 1 residues processed: 153 average time/residue: 0.2146 time to fit residues: 45.8764 Evaluate side-chains 121 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 7.9990 chunk 46 optimal weight: 8.9990 chunk 90 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 652 GLN A 683 ASN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS B 808 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.147372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.103836 restraints weight = 14593.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.107187 restraints weight = 8034.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.109404 restraints weight = 5558.151| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9443 Z= 0.155 Angle : 0.654 9.027 12819 Z= 0.336 Chirality : 0.040 0.162 1489 Planarity : 0.004 0.053 1615 Dihedral : 6.304 102.635 1320 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 1.74 % Allowed : 10.56 % Favored : 87.69 % 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: -0.34 (0.25), residues: 1170 helix: 0.54 (0.20), residues: 708 sheet: -0.46 (0.59), residues: 80 loop : -1.54 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 254 HIS 0.005 0.001 HIS B 361 PHE 0.027 0.002 PHE A 460 TYR 0.019 0.001 TYR B 541 ARG 0.004 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.07123 ( 471) hydrogen bonds : angle 4.68623 ( 1380) covalent geometry : bond 0.00295 ( 9443) covalent geometry : angle 0.65377 (12819) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 1.126 Fit side-chains REVERT: A 246 LEU cc_start: 0.8371 (mm) cc_final: 0.7976 (mm) REVERT: A 586 GLN cc_start: 0.8438 (tm-30) cc_final: 0.8139 (tm-30) REVERT: A 652 GLN cc_start: 0.7199 (OUTLIER) cc_final: 0.6690 (mp10) REVERT: A 754 THR cc_start: 0.7181 (p) cc_final: 0.6730 (p) REVERT: A 762 GLU cc_start: 0.8975 (tt0) cc_final: 0.8737 (tp30) REVERT: B 407 MET cc_start: 0.6774 (ppp) cc_final: 0.6458 (ppp) REVERT: B 433 GLU cc_start: 0.8276 (tm-30) cc_final: 0.8028 (tm-30) REVERT: B 437 LYS cc_start: 0.8440 (pttt) cc_final: 0.8114 (tmmt) REVERT: B 497 LEU cc_start: 0.8297 (tp) cc_final: 0.7975 (tt) REVERT: B 542 MET cc_start: 0.7614 (tmm) cc_final: 0.7409 (tmm) REVERT: B 547 PHE cc_start: 0.8117 (t80) cc_final: 0.7617 (t80) REVERT: B 549 THR cc_start: 0.8661 (t) cc_final: 0.8440 (t) REVERT: B 587 LYS cc_start: 0.8803 (mppt) cc_final: 0.8338 (mppt) REVERT: B 801 CYS cc_start: 0.9096 (p) cc_final: 0.8858 (p) outliers start: 17 outliers final: 8 residues processed: 149 average time/residue: 0.2005 time to fit residues: 42.4229 Evaluate side-chains 129 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 502 ASN Chi-restraints excluded: chain B residue 740 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 0.0030 chunk 36 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.144859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100715 restraints weight = 15018.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103915 restraints weight = 8415.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106031 restraints weight = 5873.369| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9443 Z= 0.186 Angle : 0.647 7.896 12819 Z= 0.329 Chirality : 0.040 0.157 1489 Planarity : 0.004 0.038 1615 Dihedral : 6.079 98.589 1319 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 3.18 % Allowed : 15.79 % Favored : 81.03 % 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: -0.11 (0.25), residues: 1170 helix: 0.77 (0.20), residues: 710 sheet: -0.46 (0.58), residues: 80 loop : -1.54 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 254 HIS 0.005 0.001 HIS B 361 PHE 0.019 0.002 PHE B 418 TYR 0.022 0.001 TYR A 386 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.06704 ( 471) hydrogen bonds : angle 4.51965 ( 1380) covalent geometry : bond 0.00420 ( 9443) covalent geometry : angle 0.64729 (12819) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 127 time to evaluate : 1.091 Fit side-chains REVERT: A 478 GLU cc_start: 0.8711 (tm-30) cc_final: 0.8218 (tm-30) REVERT: A 754 THR cc_start: 0.7254 (p) cc_final: 0.6779 (p) REVERT: A 762 GLU cc_start: 0.9018 (tt0) cc_final: 0.8768 (tp30) REVERT: B 407 MET cc_start: 0.6799 (ppp) cc_final: 0.6435 (ppp) REVERT: B 542 MET cc_start: 0.7647 (tmm) cc_final: 0.7330 (tmm) REVERT: B 547 PHE cc_start: 0.8026 (t80) cc_final: 0.7548 (t80) REVERT: B 587 LYS cc_start: 0.8822 (mppt) cc_final: 0.8482 (mppt) REVERT: B 781 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8398 (m) REVERT: B 801 CYS cc_start: 0.9089 (p) cc_final: 0.8835 (p) outliers start: 31 outliers final: 22 residues processed: 147 average time/residue: 0.2173 time to fit residues: 44.8163 Evaluate side-chains 143 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 446 GLU Chi-restraints excluded: chain B residue 495 VAL Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 77 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.144786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.100749 restraints weight = 14778.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.103951 restraints weight = 8336.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.106043 restraints weight = 5852.006| |-----------------------------------------------------------------------------| r_work (final): 0.3412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9443 Z= 0.188 Angle : 0.642 9.873 12819 Z= 0.326 Chirality : 0.040 0.159 1489 Planarity : 0.004 0.037 1615 Dihedral : 5.961 93.517 1319 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 4.10 % Allowed : 18.67 % Favored : 77.23 % 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: 0.04 (0.25), residues: 1170 helix: 0.88 (0.21), residues: 712 sheet: -0.30 (0.60), residues: 78 loop : -1.49 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 254 HIS 0.005 0.001 HIS B 361 PHE 0.016 0.002 PHE B 418 TYR 0.020 0.001 TYR A 386 ARG 0.005 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.06357 ( 471) hydrogen bonds : angle 4.37437 ( 1380) covalent geometry : bond 0.00426 ( 9443) covalent geometry : angle 0.64228 (12819) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 121 time to evaluate : 0.969 Fit side-chains REVERT: A 478 GLU cc_start: 0.8730 (tm-30) cc_final: 0.8314 (tm-30) REVERT: A 577 LEU cc_start: 0.8594 (tp) cc_final: 0.8293 (tt) REVERT: A 754 THR cc_start: 0.7121 (p) cc_final: 0.6653 (p) REVERT: A 762 GLU cc_start: 0.9008 (tt0) cc_final: 0.8804 (tp30) REVERT: B 254 TRP cc_start: 0.7769 (OUTLIER) cc_final: 0.7553 (t60) REVERT: B 542 MET cc_start: 0.7766 (tmm) cc_final: 0.7552 (tmm) REVERT: B 547 PHE cc_start: 0.8099 (t80) cc_final: 0.7851 (t80) REVERT: B 587 LYS cc_start: 0.8849 (mppt) cc_final: 0.8498 (mppt) REVERT: B 801 CYS cc_start: 0.9082 (p) cc_final: 0.8830 (p) outliers start: 40 outliers final: 31 residues processed: 146 average time/residue: 0.1929 time to fit residues: 40.1734 Evaluate side-chains 148 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 282 VAL Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 254 TRP Chi-restraints excluded: chain B residue 282 VAL Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 500 THR Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 754 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 chunk 108 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 111 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 overall best weight: 1.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN B 607 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.107651 restraints weight = 14480.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111126 restraints weight = 7814.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113408 restraints weight = 5350.003| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9443 Z= 0.130 Angle : 0.586 8.520 12819 Z= 0.294 Chirality : 0.038 0.159 1489 Planarity : 0.003 0.037 1615 Dihedral : 5.711 91.117 1319 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.97 % Allowed : 21.23 % Favored : 75.79 % 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: 0.25 (0.25), residues: 1170 helix: 1.08 (0.21), residues: 712 sheet: -0.24 (0.59), residues: 78 loop : -1.49 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 254 HIS 0.004 0.001 HIS B 361 PHE 0.015 0.001 PHE B 418 TYR 0.019 0.001 TYR B 686 ARG 0.004 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.05534 ( 471) hydrogen bonds : angle 3.94290 ( 1380) covalent geometry : bond 0.00275 ( 9443) covalent geometry : angle 0.58585 (12819) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 1.016 Fit side-chains REVERT: A 263 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8159 (mt) REVERT: A 272 MET cc_start: 0.8077 (tpt) cc_final: 0.7732 (tpp) REVERT: A 442 MET cc_start: 0.8533 (OUTLIER) cc_final: 0.7931 (ttp) REVERT: A 754 THR cc_start: 0.6979 (p) cc_final: 0.6682 (p) REVERT: B 542 MET cc_start: 0.7759 (tmm) cc_final: 0.7310 (tmm) REVERT: B 587 LYS cc_start: 0.8882 (mppt) cc_final: 0.8469 (mppt) REVERT: B 678 ASP cc_start: 0.8658 (t0) cc_final: 0.8289 (t0) outliers start: 29 outliers final: 18 residues processed: 140 average time/residue: 0.2059 time to fit residues: 40.3691 Evaluate side-chains 135 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 740 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 94 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 28 optimal weight: 0.0370 chunk 65 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 113 optimal weight: 3.9990 chunk 106 optimal weight: 6.9990 chunk 50 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 0.6658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.153949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.109399 restraints weight = 14219.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113036 restraints weight = 7527.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.115399 restraints weight = 5095.291| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.2825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9443 Z= 0.111 Angle : 0.580 12.337 12819 Z= 0.284 Chirality : 0.037 0.166 1489 Planarity : 0.003 0.038 1615 Dihedral : 5.478 86.130 1319 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 2.67 % Allowed : 21.74 % Favored : 75.59 % 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: 0.43 (0.25), residues: 1170 helix: 1.26 (0.21), residues: 714 sheet: -0.21 (0.59), residues: 78 loop : -1.48 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 254 HIS 0.002 0.001 HIS B 361 PHE 0.019 0.001 PHE A 460 TYR 0.020 0.001 TYR B 686 ARG 0.004 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.04892 ( 471) hydrogen bonds : angle 3.65125 ( 1380) covalent geometry : bond 0.00216 ( 9443) covalent geometry : angle 0.58000 (12819) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.944 Fit side-chains revert: symmetry clash REVERT: A 246 LEU cc_start: 0.8389 (mm) cc_final: 0.8067 (mm) REVERT: A 263 LEU cc_start: 0.8738 (OUTLIER) cc_final: 0.8172 (mt) REVERT: A 442 MET cc_start: 0.8552 (OUTLIER) cc_final: 0.7913 (ttp) REVERT: A 551 TYR cc_start: 0.7951 (t80) cc_final: 0.7725 (t80) REVERT: A 762 GLU cc_start: 0.9248 (tp30) cc_final: 0.9037 (tp30) REVERT: B 542 MET cc_start: 0.7774 (tmm) cc_final: 0.7311 (tmm) REVERT: B 587 LYS cc_start: 0.8856 (mppt) cc_final: 0.8358 (mppt) outliers start: 26 outliers final: 20 residues processed: 147 average time/residue: 0.2003 time to fit residues: 41.9710 Evaluate side-chains 140 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 118 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 576 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.7980 chunk 80 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 90 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 89 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.140954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.095984 restraints weight = 15015.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099617 restraints weight = 7890.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.102043 restraints weight = 5316.551| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9443 Z= 0.122 Angle : 0.580 12.723 12819 Z= 0.284 Chirality : 0.037 0.154 1489 Planarity : 0.003 0.058 1615 Dihedral : 5.358 82.782 1319 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.08 % Allowed : 23.18 % Favored : 73.74 % 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: 0.54 (0.25), residues: 1170 helix: 1.35 (0.21), residues: 714 sheet: -0.29 (0.58), residues: 78 loop : -1.43 (0.30), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 254 HIS 0.006 0.001 HIS B 361 PHE 0.022 0.001 PHE A 460 TYR 0.017 0.001 TYR B 686 ARG 0.004 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.04935 ( 471) hydrogen bonds : angle 3.63785 ( 1380) covalent geometry : bond 0.00259 ( 9443) covalent geometry : angle 0.57976 (12819) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 123 time to evaluate : 0.970 Fit side-chains REVERT: A 246 LEU cc_start: 0.8286 (mm) cc_final: 0.7883 (mm) REVERT: A 263 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8129 (mt) REVERT: A 442 MET cc_start: 0.8387 (OUTLIER) cc_final: 0.7874 (ttp) REVERT: B 542 MET cc_start: 0.7522 (tmm) cc_final: 0.7078 (tmm) REVERT: B 587 LYS cc_start: 0.8873 (mppt) cc_final: 0.8296 (mppt) REVERT: B 678 ASP cc_start: 0.8869 (t0) cc_final: 0.8371 (t0) outliers start: 30 outliers final: 25 residues processed: 142 average time/residue: 0.2074 time to fit residues: 41.3758 Evaluate side-chains 146 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 740 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 43 optimal weight: 5.9990 chunk 64 optimal weight: 20.0000 chunk 94 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.093165 restraints weight = 15279.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.096585 restraints weight = 8243.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.098886 restraints weight = 5631.511| |-----------------------------------------------------------------------------| r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9443 Z= 0.177 Angle : 0.629 10.614 12819 Z= 0.311 Chirality : 0.039 0.146 1489 Planarity : 0.004 0.069 1615 Dihedral : 5.494 85.493 1319 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.59 % Allowed : 22.67 % Favored : 73.74 % 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: 0.47 (0.25), residues: 1170 helix: 1.28 (0.21), residues: 714 sheet: -0.42 (0.57), residues: 78 loop : -1.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 488 HIS 0.009 0.001 HIS B 361 PHE 0.022 0.002 PHE A 408 TYR 0.027 0.002 TYR A 551 ARG 0.003 0.000 ARG A 648 Details of bonding type rmsd hydrogen bonds : bond 0.05502 ( 471) hydrogen bonds : angle 3.90130 ( 1380) covalent geometry : bond 0.00405 ( 9443) covalent geometry : angle 0.62863 (12819) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 119 time to evaluate : 0.955 Fit side-chains REVERT: A 263 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8113 (mt) REVERT: A 442 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.7927 (ttp) REVERT: B 241 ASP cc_start: 0.8210 (m-30) cc_final: 0.7913 (t70) REVERT: B 542 MET cc_start: 0.7564 (tmm) cc_final: 0.7124 (tmm) REVERT: B 587 LYS cc_start: 0.8882 (mppt) cc_final: 0.8353 (mppt) outliers start: 35 outliers final: 32 residues processed: 139 average time/residue: 0.2061 time to fit residues: 39.9954 Evaluate side-chains 149 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 429 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 647 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 480 ILE Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 740 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 15 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 92 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 607 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.140543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.095614 restraints weight = 14817.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.099160 restraints weight = 7909.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101492 restraints weight = 5368.734| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7766 moved from start: 0.2953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9443 Z= 0.128 Angle : 0.591 10.976 12819 Z= 0.291 Chirality : 0.038 0.147 1489 Planarity : 0.003 0.059 1615 Dihedral : 5.388 85.410 1319 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.28 % Allowed : 23.90 % Favored : 72.82 % 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: 0.55 (0.25), residues: 1170 helix: 1.34 (0.21), residues: 712 sheet: -0.41 (0.56), residues: 80 loop : -1.33 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 254 HIS 0.006 0.001 HIS B 361 PHE 0.025 0.001 PHE A 408 TYR 0.021 0.001 TYR B 686 ARG 0.003 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.05055 ( 471) hydrogen bonds : angle 3.67083 ( 1380) covalent geometry : bond 0.00277 ( 9443) covalent geometry : angle 0.59122 (12819) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 1.055 Fit side-chains REVERT: A 263 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8154 (mt) REVERT: A 442 MET cc_start: 0.8409 (OUTLIER) cc_final: 0.7861 (ttp) REVERT: A 577 LEU cc_start: 0.8400 (tp) cc_final: 0.8185 (tt) REVERT: B 542 MET cc_start: 0.7505 (tmm) cc_final: 0.7076 (tmm) REVERT: B 587 LYS cc_start: 0.8856 (mppt) cc_final: 0.8331 (mppt) REVERT: B 678 ASP cc_start: 0.8972 (t0) cc_final: 0.8509 (t0) REVERT: B 820 ASP cc_start: 0.8930 (m-30) cc_final: 0.8606 (m-30) outliers start: 32 outliers final: 27 residues processed: 141 average time/residue: 0.2048 time to fit residues: 40.8426 Evaluate side-chains 145 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 740 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 89 optimal weight: 0.8980 chunk 65 optimal weight: 0.0970 chunk 55 optimal weight: 6.9990 chunk 69 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 108 optimal weight: 4.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.139049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.093715 restraints weight = 15195.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.097236 restraints weight = 8159.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099531 restraints weight = 5550.992| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9443 Z= 0.160 Angle : 0.621 10.314 12819 Z= 0.306 Chirality : 0.039 0.144 1489 Planarity : 0.003 0.062 1615 Dihedral : 5.437 85.728 1319 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 3.08 % Allowed : 24.31 % Favored : 72.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1170 helix: 1.32 (0.21), residues: 714 sheet: -0.49 (0.55), residues: 80 loop : -1.33 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 254 HIS 0.007 0.001 HIS B 361 PHE 0.025 0.001 PHE A 408 TYR 0.021 0.001 TYR B 686 ARG 0.003 0.000 ARG A 375 Details of bonding type rmsd hydrogen bonds : bond 0.05258 ( 471) hydrogen bonds : angle 3.79354 ( 1380) covalent geometry : bond 0.00362 ( 9443) covalent geometry : angle 0.62073 (12819) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.950 Fit side-chains REVERT: A 263 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8167 (mt) REVERT: A 347 LEU cc_start: 0.7921 (OUTLIER) cc_final: 0.7451 (tt) REVERT: A 442 MET cc_start: 0.8423 (OUTLIER) cc_final: 0.7929 (ttp) REVERT: A 577 LEU cc_start: 0.8447 (tp) cc_final: 0.8228 (tt) REVERT: B 241 ASP cc_start: 0.8225 (m-30) cc_final: 0.7934 (t70) REVERT: B 542 MET cc_start: 0.7516 (tmm) cc_final: 0.7101 (tmm) REVERT: B 587 LYS cc_start: 0.8869 (mppt) cc_final: 0.8331 (mppt) REVERT: B 678 ASP cc_start: 0.8991 (t0) cc_final: 0.8497 (t0) outliers start: 30 outliers final: 26 residues processed: 135 average time/residue: 0.2125 time to fit residues: 40.5402 Evaluate side-chains 144 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 357 SER Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 442 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 559 ILE Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 607 GLN Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 680 ILE Chi-restraints excluded: chain A residue 710 MET Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 388 VAL Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 455 ASP Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 574 VAL Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 740 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 62 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 607 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.138078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.092707 restraints weight = 15206.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096091 restraints weight = 8253.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.098372 restraints weight = 5682.945| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9443 Z= 0.178 Angle : 0.641 9.768 12819 Z= 0.318 Chirality : 0.039 0.146 1489 Planarity : 0.004 0.060 1615 Dihedral : 5.554 88.025 1319 Min Nonbonded Distance : 1.869 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.69 % Allowed : 24.31 % Favored : 72.00 % 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: 0.46 (0.26), residues: 1170 helix: 1.25 (0.21), residues: 714 sheet: -0.52 (0.57), residues: 78 loop : -1.29 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 488 HIS 0.008 0.001 HIS B 361 PHE 0.028 0.002 PHE A 408 TYR 0.023 0.002 TYR B 686 ARG 0.002 0.000 ARG A 287 Details of bonding type rmsd hydrogen bonds : bond 0.05605 ( 471) hydrogen bonds : angle 3.94445 ( 1380) covalent geometry : bond 0.00407 ( 9443) covalent geometry : angle 0.64075 (12819) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2802.47 seconds wall clock time: 49 minutes 47.00 seconds (2987.00 seconds total)