Starting phenix.real_space_refine on Sun Apr 7 01:29:06 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7c_36938/04_2024/8k7c_36938_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7c_36938/04_2024/8k7c_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7c_36938/04_2024/8k7c_36938.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7c_36938/04_2024/8k7c_36938.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7c_36938/04_2024/8k7c_36938_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k7c_36938/04_2024/8k7c_36938_updated.pdb" } 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 Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "A GLU 562": "OE1" <-> "OE2" Residue "A GLU 604": "OE1" <-> "OE2" Residue "B GLU 593": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 5.31, per 1000 atoms: 0.57 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.47 Conformation dependent library (CDL) restraints added in 1.8 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... running ksdssp... Secondary structure from input PDB file: 51 helices and 6 sheets defined 62.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.11 Creating SS restraints... Processing helix chain 'A' and resid 241 through 253 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) Processing helix chain 'A' and resid 259 through 295 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 Processing helix chain 'A' and resid 299 through 316 Processing helix chain 'A' and resid 319 through 321 No H-bonds generated for 'chain 'A' and resid 319 through 321' Processing helix chain 'A' and resid 325 through 334 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 337 through 353 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) Processing helix chain 'A' and resid 358 through 362 Processing helix chain 'A' and resid 366 through 387 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) Processing helix chain 'A' and resid 391 through 403 Processing helix chain 'A' and resid 411 through 458 removed outlier: 4.062A pdb=" N GLY A 414 " --> pdb=" O ALA A 411 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ILE A 416 " --> pdb=" O PHE A 413 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 429 " --> pdb=" O THR A 426 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL A 431 " --> pdb=" O THR A 428 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 433 " --> pdb=" O VAL A 430 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N TRP A 434 " --> pdb=" O VAL A 431 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N THR A 436 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LYS A 437 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A 447 " --> pdb=" O THR A 444 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 448 " --> pdb=" O GLN A 445 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG A 452 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N VAL A 454 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ASP A 455 " --> pdb=" O ARG A 452 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU A 457 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 465 Processing helix chain 'A' and resid 471 through 519 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 530 through 568 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 629 through 636 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) Processing helix chain 'A' and resid 659 through 665 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 659 through 665' Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.716A pdb=" N ARG A 685 " --> pdb=" O ALA A 681 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N TYR A 686 " --> pdb=" O ASP A 682 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLY A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 removed outlier: 3.570A pdb=" N ALA A 702 " --> pdb=" O ALA A 698 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 710 Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 722 through 724 No H-bonds generated for 'chain 'A' and resid 722 through 724' Processing helix chain 'A' and resid 731 through 743 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 759 through 771 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 785 through 787 No H-bonds generated for 'chain 'A' and resid 785 through 787' Processing helix chain 'A' and resid 808 through 814 removed outlier: 3.922A pdb=" N ARG A 814 " --> pdb=" O ALA A 810 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 824 Processing helix chain 'B' and resid 241 through 252 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 259 through 294 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 Processing helix chain 'B' and resid 301 through 316 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 327 through 351 removed outlier: 3.585A pdb=" N THR B 331 " --> pdb=" O SER B 327 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) 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 358 through 362 Processing helix chain 'B' and resid 366 through 389 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 391 through 403 Processing helix chain 'B' and resid 411 through 438 removed outlier: 3.608A pdb=" N ILE B 429 " --> pdb=" O THR B 426 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N VAL B 431 " --> pdb=" O THR B 428 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU B 433 " --> pdb=" O VAL B 430 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TRP B 434 " --> pdb=" O VAL B 431 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LYS B 437 " --> pdb=" O TRP B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 457 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 461 through 464 No H-bonds generated for 'chain 'B' and resid 461 through 464' Processing helix chain 'B' and resid 472 through 520 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 530 through 549 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 552 through 569 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) Processing helix chain 'B' and resid 629 through 636 removed outlier: 3.669A pdb=" N LEU B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 665 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 680 through 687 removed outlier: 3.583A pdb=" N ARG B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) removed outlier: 4.951A pdb=" N GLY B 687 " --> pdb=" O ASN B 683 " (cutoff:3.500A) Processing helix chain 'B' and resid 693 through 703 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 706 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) No H-bonds generated for 'chain 'B' and resid 706 through 711' Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'B' and resid 722 through 724 No H-bonds generated for 'chain 'B' and resid 722 through 724' Processing helix chain 'B' and resid 731 through 743 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 759 through 772 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 785 through 788 removed outlier: 3.562A pdb=" N VAL B 788 " --> pdb=" O LEU B 785 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 785 through 788' Processing helix chain 'B' and resid 808 through 814 removed outlier: 4.351A pdb=" N SER B 813 " --> pdb=" O GLU B 809 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ARG B 814 " --> pdb=" O ALA B 810 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 825 Processing sheet with id= A, first strand: chain 'A' and resid 590 through 593 Processing sheet with id= B, 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: 6.599A pdb=" N GLN A 793 " --> pdb=" O ALA A 620 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL A 622 " --> pdb=" O GLN A 793 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N LEU A 795 " --> pdb=" O VAL A 622 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 666 through 669 removed outlier: 6.087A pdb=" N ILE A 747 " --> pdb=" O GLY A 667 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N VAL A 669 " --> pdb=" O ILE A 747 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N LEU A 749 " --> pdb=" O VAL A 669 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'B' and resid 590 through 593 removed outlier: 3.597A pdb=" N CYS B 646 " --> pdb=" O GLU B 593 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 778 through 781 removed outlier: 3.519A pdb=" N LEU B 619 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLN B 793 " --> pdb=" O ALA B 620 " (cutoff:3.500A) removed outlier: 7.924A pdb=" N VAL B 622 " --> pdb=" O GLN B 793 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N LEU B 795 " --> pdb=" O VAL B 622 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 666 through 669 removed outlier: 6.443A pdb=" N ILE B 747 " --> pdb=" O GLY B 667 " (cutoff:3.500A) removed outlier: 8.256A pdb=" N VAL B 669 " --> pdb=" O ILE B 747 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 749 " --> pdb=" O VAL B 669 " (cutoff:3.500A) No H-bonds generated for sheet with id= F 410 hydrogen bonds defined for protein. 1074 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: 2.34 Time building geometry restraints manager: 3.79 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: 99.15 - 106.41: 170 106.41 - 113.66: 5470 113.66 - 120.92: 4867 120.92 - 128.17: 2249 128.17 - 135.43: 63 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: 43 2.45 - 3.06: 7025 3.06 - 3.67: 12994 3.67 - 4.29: 17836 4.29 - 4.90: 28203 Nonbonded interactions: 66101 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 2.520 ... (remaining 66096 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 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: 0.810 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: 3.080 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.280 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.530 ------------------------------------------------------------------------------- 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= 0.612 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 *********************** 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 fitting. rotamer outliers: 2 poor density : 151 time to evaluate : 0.922 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: 0.2110 time to fit residues: 44.9340 Evaluate side-chains 121 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 0.969 ------------------------------------------------------------------------------- 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: 2.9990 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 46 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 652 GLN ** A 683 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 339 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1396 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= 0.267 Angle : 0.663 7.858 12819 Z= 0.340 Chirality : 0.041 0.151 1489 Planarity : 0.005 0.056 1615 Dihedral : 6.443 102.639 1320 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.46 % Allowed : 11.28 % Favored : 86.26 % 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: -0.85 (0.24), residues: 1170 helix: 0.12 (0.20), residues: 696 sheet: -0.60 (0.57), residues: 80 loop : -1.67 (0.30), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 254 HIS 0.008 0.001 HIS B 361 PHE 0.024 0.002 PHE B 565 TYR 0.018 0.002 TYR B 541 ARG 0.005 0.000 ARG A 287 *********************** 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 158 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 134 time to evaluate : 1.021 Fit side-chains REVERT: A 246 LEU cc_start: 0.8420 (mm) cc_final: 0.8039 (mm) REVERT: A 384 LEU cc_start: 0.8213 (tp) cc_final: 0.8008 (tt) REVERT: A 650 ASP cc_start: 0.8799 (t0) cc_final: 0.8178 (t0) REVERT: A 652 GLN cc_start: 0.7393 (OUTLIER) cc_final: 0.6492 (mp10) REVERT: A 754 THR cc_start: 0.7396 (p) cc_final: 0.6986 (p) REVERT: A 762 GLU cc_start: 0.8961 (tt0) cc_final: 0.8691 (tp30) REVERT: B 437 LYS cc_start: 0.8752 (pttt) cc_final: 0.7725 (mttt) REVERT: B 542 MET cc_start: 0.7671 (tmm) cc_final: 0.7429 (tmm) REVERT: B 547 PHE cc_start: 0.8045 (t80) cc_final: 0.7639 (t80) REVERT: B 587 LYS cc_start: 0.8857 (mppt) cc_final: 0.8490 (mppt) REVERT: B 710 MET cc_start: 0.9340 (mtt) cc_final: 0.9079 (mtm) REVERT: B 801 CYS cc_start: 0.9240 (p) cc_final: 0.9019 (p) outliers start: 24 outliers final: 13 residues processed: 149 average time/residue: 0.2123 time to fit residues: 44.1106 Evaluate side-chains 130 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 116 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 469 GLU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 572 THR Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 GLN 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 436 THR Chi-restraints excluded: chain B residue 502 ASN Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 781 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 10.0000 chunk 32 optimal weight: 0.0170 chunk 87 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 30.0000 chunk 105 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 10.0000 chunk 104 optimal weight: 0.3980 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 overall best weight: 0.8824 ------------------------------------------------------------------------------- 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 683 ASN B 279 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 563 ASN B 596 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9443 Z= 0.159 Angle : 0.575 8.197 12819 Z= 0.290 Chirality : 0.038 0.152 1489 Planarity : 0.004 0.044 1615 Dihedral : 5.813 91.010 1320 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.95 % Allowed : 17.64 % Favored : 80.41 % 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: 0.43 (0.20), residues: 706 sheet: -0.24 (0.59), residues: 80 loop : -1.55 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 304 HIS 0.003 0.001 HIS A 706 PHE 0.019 0.001 PHE B 565 TYR 0.014 0.001 TYR B 686 ARG 0.005 0.000 ARG A 287 *********************** 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 161 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: A 478 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8238 (tm-30) REVERT: A 577 LEU cc_start: 0.8650 (tp) cc_final: 0.8317 (tt) REVERT: A 652 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6888 (mp10) REVERT: A 754 THR cc_start: 0.7280 (p) cc_final: 0.6827 (p) REVERT: A 757 LEU cc_start: 0.9062 (OUTLIER) cc_final: 0.8826 (tt) REVERT: A 762 GLU cc_start: 0.8944 (tt0) cc_final: 0.8727 (tp30) REVERT: B 407 MET cc_start: 0.6673 (ppp) cc_final: 0.6222 (ppp) REVERT: B 437 LYS cc_start: 0.8660 (pttt) cc_final: 0.7635 (mttp) REVERT: B 542 MET cc_start: 0.7669 (tmm) cc_final: 0.7210 (tmm) REVERT: B 547 PHE cc_start: 0.8041 (t80) cc_final: 0.7633 (t80) REVERT: B 587 LYS cc_start: 0.8842 (mppt) cc_final: 0.8410 (mppt) REVERT: B 710 MET cc_start: 0.9303 (mtt) cc_final: 0.9071 (mtt) REVERT: B 801 CYS cc_start: 0.9228 (p) cc_final: 0.9024 (p) outliers start: 19 outliers final: 8 residues processed: 151 average time/residue: 0.2742 time to fit residues: 58.7886 Evaluate side-chains 132 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 122 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 757 LEU 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 436 THR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 7.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 112 optimal weight: 0.2980 chunk 55 optimal weight: 7.9990 chunk 100 optimal weight: 0.0870 chunk 30 optimal weight: 0.0370 overall best weight: 0.8038 ------------------------------------------------------------------------------- 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 652 GLN ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 279 ASN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9443 Z= 0.144 Angle : 0.555 8.678 12819 Z= 0.275 Chirality : 0.037 0.149 1489 Planarity : 0.004 0.049 1615 Dihedral : 5.477 83.105 1319 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.56 % Allowed : 20.10 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.21 (0.25), residues: 1170 helix: 0.60 (0.20), residues: 712 sheet: -0.06 (0.59), residues: 80 loop : -1.49 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 304 HIS 0.002 0.001 HIS A 706 PHE 0.018 0.001 PHE A 460 TYR 0.022 0.001 TYR A 386 ARG 0.004 0.000 ARG A 648 *********************** 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 163 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 138 time to evaluate : 1.020 Fit side-chains REVERT: A 652 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6448 (mp10) REVERT: A 754 THR cc_start: 0.7090 (p) cc_final: 0.6635 (p) REVERT: A 757 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8803 (tt) REVERT: A 762 GLU cc_start: 0.8946 (tt0) cc_final: 0.8704 (tp30) REVERT: B 386 TYR cc_start: 0.8455 (m-10) cc_final: 0.8236 (m-80) REVERT: B 437 LYS cc_start: 0.8641 (pttt) cc_final: 0.8335 (tmmt) REVERT: B 542 MET cc_start: 0.7724 (tmm) cc_final: 0.7270 (tmm) REVERT: B 547 PHE cc_start: 0.7994 (t80) cc_final: 0.7786 (t80) REVERT: B 576 ASP cc_start: 0.8635 (OUTLIER) cc_final: 0.7927 (m-30) REVERT: B 587 LYS cc_start: 0.8784 (mppt) cc_final: 0.8450 (mppt) REVERT: B 668 VAL cc_start: 0.9288 (t) cc_final: 0.9034 (p) REVERT: B 710 MET cc_start: 0.9266 (mtt) cc_final: 0.9028 (mtt) outliers start: 25 outliers final: 16 residues processed: 152 average time/residue: 0.2125 time to fit residues: 45.1930 Evaluate side-chains 145 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 126 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 474 GLU Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 757 LEU 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 436 THR Chi-restraints excluded: chain B residue 550 TYR Chi-restraints excluded: chain B residue 576 ASP Chi-restraints excluded: chain B residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 83 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 77 optimal weight: 0.0770 chunk 0 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 100 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 overall best weight: 2.1944 ------------------------------------------------------------------------------- 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 652 GLN ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9443 Z= 0.234 Angle : 0.582 7.914 12819 Z= 0.291 Chirality : 0.039 0.150 1489 Planarity : 0.004 0.045 1615 Dihedral : 5.472 79.372 1319 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.00 % Allowed : 21.03 % Favored : 74.97 % 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: -0.14 (0.25), residues: 1170 helix: 0.64 (0.20), residues: 714 sheet: -0.05 (0.59), residues: 78 loop : -1.43 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 488 HIS 0.006 0.001 HIS B 361 PHE 0.018 0.001 PHE B 418 TYR 0.021 0.001 TYR A 386 ARG 0.005 0.000 ARG A 435 *********************** 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 163 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 124 time to evaluate : 1.029 Fit side-chains REVERT: A 652 GLN cc_start: 0.7435 (OUTLIER) cc_final: 0.6382 (mp10) REVERT: A 754 THR cc_start: 0.7178 (p) cc_final: 0.6691 (p) REVERT: A 757 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8862 (tt) REVERT: A 762 GLU cc_start: 0.8964 (tt0) cc_final: 0.8731 (tp30) REVERT: B 254 TRP cc_start: 0.7772 (OUTLIER) cc_final: 0.7549 (t60) REVERT: B 437 LYS cc_start: 0.8700 (pttt) cc_final: 0.8373 (tmmt) REVERT: B 542 MET cc_start: 0.7730 (tmm) cc_final: 0.7265 (tmm) REVERT: B 547 PHE cc_start: 0.8026 (t80) cc_final: 0.7803 (t80) REVERT: B 587 LYS cc_start: 0.8875 (mppt) cc_final: 0.8497 (mppt) REVERT: B 710 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.9004 (mtt) outliers start: 39 outliers final: 23 residues processed: 152 average time/residue: 0.2094 time to fit residues: 44.9936 Evaluate side-chains 145 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 118 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 444 THR 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 632 ILE Chi-restraints excluded: chain A residue 642 ILE Chi-restraints excluded: chain A residue 652 GLN Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 254 TRP 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 436 THR Chi-restraints excluded: chain B residue 541 TYR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 27 optimal weight: 8.9990 chunk 112 optimal weight: 4.9990 chunk 93 optimal weight: 0.7980 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 108 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- 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 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9443 Z= 0.209 Angle : 0.581 10.022 12819 Z= 0.286 Chirality : 0.038 0.151 1489 Planarity : 0.004 0.047 1615 Dihedral : 5.385 74.784 1319 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.90 % Allowed : 21.95 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.25), residues: 1170 helix: 0.66 (0.20), residues: 714 sheet: 0.04 (0.59), residues: 78 loop : -1.38 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 254 HIS 0.008 0.001 HIS B 361 PHE 0.018 0.001 PHE B 418 TYR 0.021 0.001 TYR B 686 ARG 0.004 0.000 ARG A 435 *********************** 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 163 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 125 time to evaluate : 0.944 Fit side-chains REVERT: A 246 LEU cc_start: 0.8411 (mm) cc_final: 0.8078 (mm) REVERT: A 347 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7604 (tt) REVERT: A 754 THR cc_start: 0.7173 (p) cc_final: 0.6891 (p) REVERT: A 757 LEU cc_start: 0.9108 (OUTLIER) cc_final: 0.8882 (tt) REVERT: A 762 GLU cc_start: 0.8922 (tt0) cc_final: 0.8670 (tt0) REVERT: B 254 TRP cc_start: 0.7742 (OUTLIER) cc_final: 0.7520 (t60) REVERT: B 386 TYR cc_start: 0.8454 (m-80) cc_final: 0.8152 (m-80) REVERT: B 437 LYS cc_start: 0.8733 (pttt) cc_final: 0.8399 (tmmt) REVERT: B 542 MET cc_start: 0.7766 (tmm) cc_final: 0.7305 (tmm) REVERT: B 547 PHE cc_start: 0.8037 (t80) cc_final: 0.7834 (t80) REVERT: B 587 LYS cc_start: 0.8872 (mppt) cc_final: 0.8509 (mppt) REVERT: B 710 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.9010 (mtt) outliers start: 38 outliers final: 27 residues processed: 150 average time/residue: 0.2162 time to fit residues: 45.2977 Evaluate side-chains 151 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 120 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 VAL 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 430 VAL Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 642 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 757 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain B residue 254 TRP 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 436 THR 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 613 VAL Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 740 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 5.9990 chunk 111 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9443 Z= 0.299 Angle : 0.630 7.501 12819 Z= 0.313 Chirality : 0.040 0.147 1489 Planarity : 0.004 0.052 1615 Dihedral : 5.489 72.096 1319 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 4.82 % Allowed : 22.05 % Favored : 73.13 % 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: -0.10 (0.25), residues: 1170 helix: 0.66 (0.21), residues: 708 sheet: 0.04 (0.59), residues: 78 loop : -1.38 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 488 HIS 0.009 0.001 HIS B 361 PHE 0.020 0.002 PHE B 418 TYR 0.024 0.001 TYR B 686 ARG 0.004 0.000 ARG A 435 *********************** 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 165 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 118 time to evaluate : 0.813 Fit side-chains REVERT: A 246 LEU cc_start: 0.8411 (mm) cc_final: 0.7989 (mm) REVERT: A 263 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8235 (mt) REVERT: A 272 MET cc_start: 0.8058 (tpt) cc_final: 0.7845 (tpp) REVERT: A 478 GLU cc_start: 0.8631 (tm-30) cc_final: 0.8145 (tm-30) REVERT: A 754 THR cc_start: 0.7286 (p) cc_final: 0.6988 (p) REVERT: A 757 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8911 (tt) REVERT: A 762 GLU cc_start: 0.8898 (tt0) cc_final: 0.8696 (tt0) REVERT: B 254 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.6544 (t60) REVERT: B 437 LYS cc_start: 0.8783 (pttt) cc_final: 0.8447 (tmmt) REVERT: B 542 MET cc_start: 0.7759 (tmm) cc_final: 0.7294 (tmm) REVERT: B 547 PHE cc_start: 0.8044 (t80) cc_final: 0.7814 (t80) REVERT: B 587 LYS cc_start: 0.8932 (mppt) cc_final: 0.8551 (mppt) REVERT: B 710 MET cc_start: 0.9282 (OUTLIER) cc_final: 0.9018 (mtt) outliers start: 47 outliers final: 34 residues processed: 148 average time/residue: 0.2136 time to fit residues: 44.6922 Evaluate side-chains 157 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 119 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 267 ILE 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 432 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 480 ILE Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 642 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 757 LEU Chi-restraints excluded: chain B residue 254 TRP Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 345 VAL Chi-restraints excluded: chain B residue 357 SER Chi-restraints excluded: chain B residue 361 HIS 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 436 THR 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 613 VAL Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 740 THR Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 7.9990 chunk 21 optimal weight: 0.9990 chunk 71 optimal weight: 0.0000 chunk 76 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 9.9990 chunk 101 optimal weight: 0.0470 chunk 107 optimal weight: 0.9980 chunk 97 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 overall best weight: 0.5484 ------------------------------------------------------------------------------- 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 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9443 Z= 0.139 Angle : 0.565 10.582 12819 Z= 0.275 Chirality : 0.037 0.150 1489 Planarity : 0.003 0.041 1615 Dihedral : 5.096 63.600 1319 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.46 % Allowed : 24.72 % 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: 0.08 (0.25), residues: 1170 helix: 0.80 (0.21), residues: 710 sheet: 0.10 (0.59), residues: 78 loop : -1.30 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 254 HIS 0.004 0.001 HIS B 361 PHE 0.025 0.001 PHE A 460 TYR 0.030 0.001 TYR A 386 ARG 0.003 0.000 ARG A 435 *********************** 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 146 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 122 time to evaluate : 1.046 Fit side-chains REVERT: A 246 LEU cc_start: 0.8416 (mm) cc_final: 0.7977 (mm) REVERT: A 263 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8218 (mt) REVERT: A 757 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8876 (tt) REVERT: B 542 MET cc_start: 0.7720 (tmm) cc_final: 0.7273 (tmm) REVERT: B 587 LYS cc_start: 0.8879 (mppt) cc_final: 0.8476 (mppt) REVERT: B 710 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8982 (mtt) outliers start: 24 outliers final: 15 residues processed: 136 average time/residue: 0.2210 time to fit residues: 41.8735 Evaluate side-chains 133 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 444 THR Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 558 PHE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 766 GLN Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 436 THR 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 613 VAL Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.7980 chunk 62 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 98 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9443 Z= 0.155 Angle : 0.569 11.577 12819 Z= 0.273 Chirality : 0.037 0.149 1489 Planarity : 0.004 0.072 1615 Dihedral : 4.966 59.219 1319 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.36 % Allowed : 25.23 % Favored : 72.41 % 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: 0.28 (0.25), residues: 1170 helix: 0.93 (0.21), residues: 700 sheet: 0.15 (0.59), residues: 78 loop : -1.09 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 254 HIS 0.002 0.001 HIS A 352 PHE 0.023 0.001 PHE A 460 TYR 0.027 0.001 TYR A 386 ARG 0.003 0.000 ARG A 648 *********************** 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 142 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 119 time to evaluate : 1.085 Fit side-chains REVERT: A 263 LEU cc_start: 0.8677 (OUTLIER) cc_final: 0.8231 (mt) REVERT: B 542 MET cc_start: 0.7665 (tmm) cc_final: 0.7228 (tmm) REVERT: B 587 LYS cc_start: 0.8843 (mppt) cc_final: 0.8454 (mppt) REVERT: B 710 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8974 (mtt) outliers start: 23 outliers final: 19 residues processed: 132 average time/residue: 0.2133 time to fit residues: 39.4660 Evaluate side-chains 136 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 444 THR 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 613 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 436 THR 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 613 VAL Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 4.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 106 optimal weight: 0.6980 chunk 92 optimal weight: 6.9990 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 56 optimal weight: 0.0970 chunk 73 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 28 optimal weight: 0.0010 overall best weight: 0.5184 ------------------------------------------------------------------------------- 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** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9443 Z= 0.133 Angle : 0.560 10.330 12819 Z= 0.270 Chirality : 0.036 0.151 1489 Planarity : 0.004 0.059 1615 Dihedral : 4.723 49.170 1319 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 2.36 % Allowed : 25.33 % Favored : 72.31 % 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: 0.40 (0.25), residues: 1170 helix: 1.04 (0.21), residues: 700 sheet: 0.24 (0.60), residues: 78 loop : -1.07 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 254 HIS 0.005 0.001 HIS B 361 PHE 0.021 0.001 PHE B 418 TYR 0.026 0.001 TYR A 386 ARG 0.003 0.000 ARG A 648 ********************** 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 149 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.150 Fit side-chains REVERT: A 263 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8227 (mt) REVERT: A 435 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.6939 (ttm-80) REVERT: B 386 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7193 (t80) REVERT: B 542 MET cc_start: 0.7647 (tmm) cc_final: 0.7183 (tmm) REVERT: B 587 LYS cc_start: 0.8772 (mppt) cc_final: 0.8375 (mppt) REVERT: B 710 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.8986 (mtt) outliers start: 23 outliers final: 18 residues processed: 140 average time/residue: 0.2295 time to fit residues: 44.3351 Evaluate side-chains 139 residues out of total 992 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 118 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 398 ILE Chi-restraints excluded: chain A residue 444 THR 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 613 VAL Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 669 VAL Chi-restraints excluded: chain A residue 741 ILE Chi-restraints excluded: chain B residue 386 TYR Chi-restraints excluded: chain B residue 387 LEU Chi-restraints excluded: chain B residue 398 ILE Chi-restraints excluded: chain B residue 436 THR 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 613 VAL Chi-restraints excluded: chain B residue 710 MET Chi-restraints excluded: chain B residue 801 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 chunk 94 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.0020 chunk 80 optimal weight: 0.8980 chunk 5 optimal weight: 6.9990 chunk 66 optimal weight: 6.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- 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 596 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 443 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 484 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 596 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.157202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.111986 restraints weight = 14302.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115723 restraints weight = 7575.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.117984 restraints weight = 5158.553| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 9443 Z= 0.140 Angle : 0.560 9.951 12819 Z= 0.267 Chirality : 0.037 0.148 1489 Planarity : 0.003 0.051 1615 Dihedral : 4.614 45.385 1319 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.26 % Allowed : 25.44 % Favored : 72.31 % 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: 0.51 (0.26), residues: 1170 helix: 1.12 (0.21), residues: 700 sheet: 0.30 (0.60), residues: 78 loop : -1.03 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 254 HIS 0.005 0.001 HIS B 361 PHE 0.022 0.001 PHE A 408 TYR 0.027 0.001 TYR A 386 ARG 0.003 0.000 ARG A 648 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1912.26 seconds wall clock time: 35 minutes 38.71 seconds (2138.71 seconds total)