Starting phenix.real_space_refine on Sun Mar 17 15:08:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwg_35057/03_2024/8hwg_35057_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwg_35057/03_2024/8hwg_35057.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwg_35057/03_2024/8hwg_35057.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwg_35057/03_2024/8hwg_35057.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwg_35057/03_2024/8hwg_35057_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwg_35057/03_2024/8hwg_35057_updated.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 22 5.49 5 Mg 6 5.21 5 S 98 5.16 5 C 11445 2.51 5 N 3085 2.21 5 O 3454 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 431": "OD1" <-> "OD2" Residue "C ASP 534": "OD1" <-> "OD2" Residue "C ASP 603": "OD1" <-> "OD2" Residue "C ASP 611": "OD1" <-> "OD2" Residue "C GLU 691": "OE1" <-> "OE2" Residue "B ASP 424": "OD1" <-> "OD2" Residue "B ASP 537": "OD1" <-> "OD2" Residue "B PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 603": "OD1" <-> "OD2" Residue "B ASP 611": "OD1" <-> "OD2" Residue "B ASP 643": "OD1" <-> "OD2" Residue "D GLU 343": "OE1" <-> "OE2" Residue "D GLU 360": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D GLU 393": "OE1" <-> "OE2" Residue "D PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 500": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D ASP 534": "OD1" <-> "OD2" Residue "D ASP 643": "OD1" <-> "OD2" Residue "D GLU 653": "OE1" <-> "OE2" Residue "D ASP 656": "OD1" <-> "OD2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A ASP 454": "OD1" <-> "OD2" Residue "A GLU 459": "OE1" <-> "OE2" Residue "A ASP 522": "OD1" <-> "OD2" Residue "A PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 526": "OE1" <-> "OE2" Residue "A ASP 572": "OD1" <-> "OD2" Residue "A GLU 579": "OE1" <-> "OE2" Residue "A ASP 603": "OD1" <-> "OD2" Residue "A ASP 656": "OD1" <-> "OD2" Residue "A TYR 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 360": "OE1" <-> "OE2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 572": "OD1" <-> "OD2" Residue "F TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 653": "OE1" <-> "OE2" Residue "F TYR 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 360": "OE1" <-> "OE2" Residue "E ASP 402": "OD1" <-> "OD2" Residue "E ASP 448": "OD1" <-> "OD2" Residue "E GLU 457": "OE1" <-> "OE2" Residue "E GLU 460": "OE1" <-> "OE2" Residue "E GLU 480": "OE1" <-> "OE2" Residue "E ASP 522": "OD1" <-> "OD2" Residue "E GLU 579": "OE1" <-> "OE2" Residue "E GLU 653": "OE1" <-> "OE2" Residue "E TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 691": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 18110 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2996 Classifications: {'peptide': 372} Link IDs: {'PTRANS': 18, 'TRANS': 353} Chain: "B" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2972 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "D" Number of atoms: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3051 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} Chain: "A" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2972 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "F" Number of atoms: 2843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2843 Classifications: {'peptide': 352} Link IDs: {'PTRANS': 14, 'TRANS': 337} Chain breaks: 1 Chain: "E" Number of atoms: 2972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2972 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 17, 'TRANS': 351} Chain: "S" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 120 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.32, per 1000 atoms: 0.51 Number of scatterers: 18110 At special positions: 0 Unit cell: (125.925, 131.4, 120.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 98 16.00 P 22 15.00 Mg 6 11.99 O 3454 8.00 N 3085 7.00 C 11445 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: 6.42 Conformation dependent library (CDL) restraints added in 3.0 seconds 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4204 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 91 helices and 25 sheets defined 35.7% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.618A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 370 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 377 through 383 removed outlier: 3.781A pdb=" N SER C 381 " --> pdb=" O LYS C 377 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N GLU C 382 " --> pdb=" O GLU C 378 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 383 " --> pdb=" O TYR C 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 377 through 383' Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.864A pdb=" N LYS C 390 " --> pdb=" O PRO C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 477 through 490 removed outlier: 4.605A pdb=" N LEU C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 523 removed outlier: 7.390A pdb=" N ASP C 522 " --> pdb=" O SER C 518 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N LEU C 523 " --> pdb=" O ALA C 519 " (cutoff:3.500A) Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.578A pdb=" N THR C 533 " --> pdb=" O THR C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 removed outlier: 5.143A pdb=" N MET C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.715A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 641 removed outlier: 4.474A pdb=" N GLU C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ALA C 638 " --> pdb=" O GLY C 635 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ASN C 641 " --> pdb=" O ALA C 638 " (cutoff:3.500A) Processing helix chain 'C' and resid 655 through 660 Processing helix chain 'C' and resid 665 through 679 removed outlier: 3.555A pdb=" N LEU C 669 " --> pdb=" O ARG C 665 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS C 678 " --> pdb=" O LYS C 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 364 through 370 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 377 through 384 removed outlier: 3.584A pdb=" N SER B 381 " --> pdb=" O LYS B 377 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLU B 382 " --> pdb=" O GLU B 378 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N LEU B 383 " --> pdb=" O TYR B 379 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N LEU B 384 " --> pdb=" O SER B 380 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 377 through 384' Processing helix chain 'B' and resid 386 through 399 removed outlier: 3.731A pdb=" N LYS B 390 " --> pdb=" O PRO B 386 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N VAL B 392 " --> pdb=" O LYS B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 removed outlier: 3.573A pdb=" N LYS B 434 " --> pdb=" O ASP B 431 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 476 through 490 removed outlier: 3.899A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 4.963A pdb=" N LEU B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 523 removed outlier: 7.495A pdb=" N ASP B 522 " --> pdb=" O SER B 518 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N LEU B 523 " --> pdb=" O ALA B 519 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 531 No H-bonds generated for 'chain 'B' and resid 529 through 531' Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.648A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 618 No H-bonds generated for 'chain 'B' and resid 615 through 618' Processing helix chain 'B' and resid 636 through 639 No H-bonds generated for 'chain 'B' and resid 636 through 639' Processing helix chain 'B' and resid 655 through 660 Processing helix chain 'B' and resid 665 through 679 removed outlier: 3.657A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.612A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 374 removed outlier: 3.641A pdb=" N ARG D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N HIS D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLN D 374 " --> pdb=" O SER D 370 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 384 removed outlier: 4.343A pdb=" N GLU D 382 " --> pdb=" O GLU D 378 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N LEU D 383 " --> pdb=" O TYR D 379 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LEU D 384 " --> pdb=" O SER D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 399 Processing helix chain 'D' and resid 456 through 468 Processing helix chain 'D' and resid 473 through 490 removed outlier: 3.867A pdb=" N LYS D 476 " --> pdb=" O ASP D 473 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N LYS D 477 " --> pdb=" O GLU D 474 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N ASN D 478 " --> pdb=" O ASN D 475 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG D 479 " --> pdb=" O LYS D 476 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU D 490 " --> pdb=" O SER D 487 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 523 removed outlier: 7.333A pdb=" N ASP D 522 " --> pdb=" O SER D 518 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N LEU D 523 " --> pdb=" O ALA D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 542 through 545 No H-bonds generated for 'chain 'D' and resid 542 through 545' Processing helix chain 'D' and resid 571 through 578 removed outlier: 3.933A pdb=" N THR D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 620 removed outlier: 3.610A pdb=" N ARG D 619 " --> pdb=" O ASN D 615 " (cutoff:3.500A) removed outlier: 4.587A pdb=" N ARG D 620 " --> pdb=" O ALA D 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 615 through 620' Processing helix chain 'D' and resid 636 through 640 Processing helix chain 'D' and resid 657 through 660 No H-bonds generated for 'chain 'D' and resid 657 through 660' Processing helix chain 'D' and resid 665 through 679 Processing helix chain 'D' and resid 690 through 692 No H-bonds generated for 'chain 'D' and resid 690 through 692' Processing helix chain 'D' and resid 694 through 699 Processing helix chain 'A' and resid 325 through 335 removed outlier: 3.535A pdb=" N ALA A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 370 Processing helix chain 'A' and resid 377 through 384 removed outlier: 4.361A pdb=" N GLU A 382 " --> pdb=" O GLU A 378 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 383 " --> pdb=" O TYR A 379 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU A 384 " --> pdb=" O SER A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 399 Processing helix chain 'A' and resid 430 through 432 No H-bonds generated for 'chain 'A' and resid 430 through 432' Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 477 through 489 removed outlier: 3.858A pdb=" N LEU A 481 " --> pdb=" O LYS A 477 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N CYS A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 7.656A pdb=" N ASP A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.819A pdb=" N THR A 533 " --> pdb=" O THR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 545 No H-bonds generated for 'chain 'A' and resid 542 through 545' Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 618 through 620 No H-bonds generated for 'chain 'A' and resid 618 through 620' Processing helix chain 'A' and resid 633 through 639 removed outlier: 3.825A pdb=" N ARG A 636 " --> pdb=" O PRO A 633 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA A 638 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.985A pdb=" N LYS A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TYR A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 335 Processing helix chain 'F' and resid 364 through 373 removed outlier: 3.677A pdb=" N LEU F 369 " --> pdb=" O THR F 365 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG F 372 " --> pdb=" O ILE F 368 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N HIS F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 383 removed outlier: 3.614A pdb=" N SER F 381 " --> pdb=" O LYS F 377 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N GLU F 382 " --> pdb=" O GLU F 378 " (cutoff:3.500A) removed outlier: 4.445A pdb=" N LEU F 383 " --> pdb=" O TYR F 379 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 377 through 383' Processing helix chain 'F' and resid 389 through 399 Processing helix chain 'F' and resid 431 through 434 Processing helix chain 'F' and resid 456 through 461 removed outlier: 3.769A pdb=" N GLU F 460 " --> pdb=" O PRO F 456 " (cutoff:3.500A) Processing helix chain 'F' and resid 464 through 468 Processing helix chain 'F' and resid 477 through 490 removed outlier: 4.736A pdb=" N LEU F 490 " --> pdb=" O LEU F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 520 Processing helix chain 'F' and resid 529 through 531 No H-bonds generated for 'chain 'F' and resid 529 through 531' Processing helix chain 'F' and resid 542 through 547 removed outlier: 4.066A pdb=" N ALA F 545 " --> pdb=" O PRO F 542 " (cutoff:3.500A) removed outlier: 5.284A pdb=" N ASN F 546 " --> pdb=" O PHE F 543 " (cutoff:3.500A) Processing helix chain 'F' and resid 572 through 576 Processing helix chain 'F' and resid 615 through 620 removed outlier: 3.789A pdb=" N ARG F 620 " --> pdb=" O ALA F 616 " (cutoff:3.500A) Processing helix chain 'F' and resid 633 through 640 removed outlier: 5.810A pdb=" N GLU F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ALA F 638 " --> pdb=" O GLY F 635 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLU F 640 " --> pdb=" O GLU F 637 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 660 removed outlier: 3.578A pdb=" N ASP F 656 " --> pdb=" O GLU F 653 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ILE F 659 " --> pdb=" O ASP F 656 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLN F 660 " --> pdb=" O GLY F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 665 through 679 Processing helix chain 'E' and resid 328 through 335 Processing helix chain 'E' and resid 368 through 374 removed outlier: 5.114A pdb=" N HIS E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N GLN E 374 " --> pdb=" O SER E 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 380 No H-bonds generated for 'chain 'E' and resid 377 through 380' Processing helix chain 'E' and resid 389 through 399 Processing helix chain 'E' and resid 430 through 434 removed outlier: 3.501A pdb=" N LYS E 434 " --> pdb=" O ASP E 431 " (cutoff:3.500A) Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'E' and resid 477 through 490 removed outlier: 4.583A pdb=" N LEU E 490 " --> pdb=" O LEU E 486 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 520 Processing helix chain 'E' and resid 529 through 533 removed outlier: 3.840A pdb=" N THR E 533 " --> pdb=" O THR E 530 " (cutoff:3.500A) Processing helix chain 'E' and resid 542 through 547 removed outlier: 4.128A pdb=" N ASN E 546 " --> pdb=" O PRO E 542 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N MET E 547 " --> pdb=" O PHE E 543 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 542 through 547' Processing helix chain 'E' and resid 571 through 576 Processing helix chain 'E' and resid 618 through 620 No H-bonds generated for 'chain 'E' and resid 618 through 620' Processing helix chain 'E' and resid 633 through 640 removed outlier: 3.876A pdb=" N ARG E 636 " --> pdb=" O PRO E 633 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N GLU E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA E 638 " --> pdb=" O GLY E 635 " (cutoff:3.500A) Processing helix chain 'E' and resid 654 through 661 Processing helix chain 'E' and resid 665 through 679 Processing sheet with id= A, first strand: chain 'C' and resid 339 through 341 Processing sheet with id= B, first strand: chain 'C' and resid 412 through 414 removed outlier: 3.525A pdb=" N MET C 426 " --> pdb=" O ASP C 421 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 602 through 604 removed outlier: 3.683A pdb=" N GLY C 503 " --> pdb=" O THR C 604 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 524 through 526 removed outlier: 6.301A pdb=" N SER C 552 " --> pdb=" O VAL C 525 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N THR C 599 " --> pdb=" O VAL C 553 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'C' and resid 629 through 631 Processing sheet with id= F, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.967A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 621 through 626 removed outlier: 6.270A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 600 " --> pdb=" O THR B 499 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N PHE B 501 " --> pdb=" O ILE B 600 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ILE B 602 " --> pdb=" O PHE B 501 " (cutoff:3.500A) removed outlier: 7.905A pdb=" N GLY B 503 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N THR B 604 " --> pdb=" O GLY B 503 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 581 through 583 Processing sheet with id= I, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.496A pdb=" N LYS B 647 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N SER B 631 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LYS B 649 " --> pdb=" O SER B 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'D' and resid 339 through 341 Processing sheet with id= K, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.947A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 621 through 626 removed outlier: 6.356A pdb=" N LEU D 498 " --> pdb=" O ALA D 622 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL D 624 " --> pdb=" O LEU D 498 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N PHE D 500 " --> pdb=" O VAL D 624 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N PHE D 626 " --> pdb=" O PHE D 500 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N PHE D 502 " --> pdb=" O PHE D 626 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE D 600 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N PHE D 501 " --> pdb=" O ILE D 600 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ILE D 602 " --> pdb=" O PHE D 501 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY D 503 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N THR D 604 " --> pdb=" O GLY D 503 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N SER D 556 " --> pdb=" O THR D 527 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 581 through 583 Processing sheet with id= N, first strand: chain 'A' and resid 339 through 341 Processing sheet with id= O, first strand: chain 'A' and resid 412 through 414 Processing sheet with id= P, first strand: chain 'A' and resid 621 through 626 removed outlier: 5.918A pdb=" N LEU A 498 " --> pdb=" O ALA A 622 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL A 624 " --> pdb=" O LEU A 498 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N PHE A 500 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N PHE A 626 " --> pdb=" O PHE A 500 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N PHE A 502 " --> pdb=" O PHE A 626 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE A 600 " --> pdb=" O THR A 499 " (cutoff:3.500A) removed outlier: 7.515A pdb=" N PHE A 501 " --> pdb=" O ILE A 600 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE A 602 " --> pdb=" O PHE A 501 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N GLY A 503 " --> pdb=" O ILE A 602 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 339 through 341 removed outlier: 3.545A pdb=" N ILE F 351 " --> pdb=" O SER F 354 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 412 through 415 Processing sheet with id= S, first strand: chain 'F' and resid 500 through 502 removed outlier: 3.550A pdb=" N PHE F 502 " --> pdb=" O VAL F 624 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'F' and resid 552 through 554 removed outlier: 5.926A pdb=" N THR F 599 " --> pdb=" O VAL F 553 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 629 through 631 Processing sheet with id= V, first strand: chain 'E' and resid 339 through 341 Processing sheet with id= W, first strand: chain 'E' and resid 412 through 414 Processing sheet with id= X, first strand: chain 'E' and resid 602 through 604 removed outlier: 3.554A pdb=" N THR E 604 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLY E 503 " --> pdb=" O THR E 604 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'E' and resid 629 through 631 433 hydrogen bonds defined for protein. 1203 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: 4.67 Time building geometry restraints manager: 7.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.34: 5823 1.34 - 1.49: 4730 1.49 - 1.64: 7794 1.64 - 1.80: 47 1.80 - 1.95: 93 Bond restraints: 18487 Sorted by residual: bond pdb=" CA SER E 455 " pdb=" C SER E 455 " ideal model delta sigma weight residual 1.526 1.627 -0.102 1.47e-02 4.63e+03 4.77e+01 bond pdb=" N SER E 455 " pdb=" CA SER E 455 " ideal model delta sigma weight residual 1.456 1.499 -0.042 9.80e-03 1.04e+04 1.88e+01 bond pdb=" C ASP E 454 " pdb=" N SER E 455 " ideal model delta sigma weight residual 1.327 1.366 -0.040 1.05e-02 9.07e+03 1.44e+01 bond pdb=" CA CYS E 489 " pdb=" C CYS E 489 " ideal model delta sigma weight residual 1.523 1.565 -0.042 1.34e-02 5.57e+03 9.91e+00 bond pdb=" C SER E 455 " pdb=" O SER E 455 " ideal model delta sigma weight residual 1.234 1.190 0.045 1.56e-02 4.11e+03 8.19e+00 ... (remaining 18482 not shown) Histogram of bond angle deviations from ideal: 97.17 - 104.96: 359 104.96 - 112.74: 9836 112.74 - 120.52: 7832 120.52 - 128.31: 6894 128.31 - 136.09: 99 Bond angle restraints: 25020 Sorted by residual: angle pdb=" N ILE F 364 " pdb=" CA ILE F 364 " pdb=" C ILE F 364 " ideal model delta sigma weight residual 110.42 105.30 5.12 9.60e-01 1.09e+00 2.85e+01 angle pdb=" C GLY F 323 " pdb=" N ASN F 324 " pdb=" CA ASN F 324 " ideal model delta sigma weight residual 121.54 129.24 -7.70 1.91e+00 2.74e-01 1.63e+01 angle pdb=" CA SER E 455 " pdb=" C SER E 455 " pdb=" N PRO E 456 " ideal model delta sigma weight residual 117.62 121.55 -3.93 1.03e+00 9.43e-01 1.46e+01 angle pdb=" O GLU F 361 " pdb=" C GLU F 361 " pdb=" N PRO F 362 " ideal model delta sigma weight residual 121.72 118.21 3.51 9.80e-01 1.04e+00 1.28e+01 angle pdb=" CA ASP A 603 " pdb=" CB ASP A 603 " pdb=" CG ASP A 603 " ideal model delta sigma weight residual 112.60 115.95 -3.35 1.00e+00 1.00e+00 1.12e+01 ... (remaining 25015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.18: 10657 33.18 - 66.35: 593 66.35 - 99.53: 36 99.53 - 132.71: 0 132.71 - 165.88: 4 Dihedral angle restraints: 11290 sinusoidal: 4811 harmonic: 6479 Sorted by residual: dihedral pdb=" C5' ADP E1001 " pdb=" O5' ADP E1001 " pdb=" PA ADP E1001 " pdb=" O2A ADP E1001 " ideal model delta sinusoidal sigma weight residual -60.00 -149.54 89.54 1 2.00e+01 2.50e-03 2.38e+01 dihedral pdb=" CA LYS E 366 " pdb=" C LYS E 366 " pdb=" N LEU E 367 " pdb=" CA LEU E 367 " ideal model delta harmonic sigma weight residual 180.00 156.18 23.82 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" O1A AGS C1001 " pdb=" O3A AGS C1001 " pdb=" PA AGS C1001 " pdb=" PB AGS C1001 " ideal model delta sinusoidal sigma weight residual 292.27 126.39 165.88 1 3.00e+01 1.11e-03 2.10e+01 ... (remaining 11287 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2451 0.067 - 0.133: 337 0.133 - 0.200: 3 0.200 - 0.266: 1 0.266 - 0.333: 1 Chirality restraints: 2793 Sorted by residual: chirality pdb=" CA SER E 455 " pdb=" N SER E 455 " pdb=" C SER E 455 " pdb=" CB SER E 455 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.77e+00 chirality pdb=" CA ILE F 364 " pdb=" N ILE F 364 " pdb=" C ILE F 364 " pdb=" CB ILE F 364 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA ILE A 683 " pdb=" N ILE A 683 " pdb=" C ILE A 683 " pdb=" CB ILE A 683 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.06e-01 ... (remaining 2790 not shown) Planarity restraints: 3162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 361 " -0.045 5.00e-02 4.00e+02 6.81e-02 7.41e+00 pdb=" N PRO D 362 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 361 " 0.033 5.00e-02 4.00e+02 4.97e-02 3.95e+00 pdb=" N PRO B 362 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO B 362 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 362 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS D 484 " 0.010 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C LYS D 484 " -0.033 2.00e-02 2.50e+03 pdb=" O LYS D 484 " 0.012 2.00e-02 2.50e+03 pdb=" N THR D 485 " 0.011 2.00e-02 2.50e+03 ... (remaining 3159 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.45: 82 2.45 - 3.06: 10890 3.06 - 3.67: 25842 3.67 - 4.29: 40870 4.29 - 4.90: 68092 Nonbonded interactions: 145776 Sorted by model distance: nonbonded pdb=" OG SER C 510 " pdb="MG MG C1002 " model vdw 1.832 2.170 nonbonded pdb=" O3G AGS B1001 " pdb="MG MG B1002 " model vdw 1.990 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A1002 " model vdw 2.011 2.170 nonbonded pdb=" O3G AGS D1001 " pdb="MG MG D1002 " model vdw 2.013 2.170 nonbonded pdb=" O3G AGS A1001 " pdb="MG MG A1002 " model vdw 2.024 2.170 ... (remaining 145771 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 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'B' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'C' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'D' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'E' and (resid 323 through 580 or resid 594 through 687 or resid 1002)) selection = (chain 'F' and (resid 323 through 687 or resid 1002)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.920 Set stop_for_unknowns flag: 0.010 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: 8.030 Check model and map are aligned: 0.240 Set scattering table: 0.140 Process input model: 46.370 Find NCS groups from input model: 1.360 Set up NCS constraints: 0.070 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:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8527 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 : 0.004 0.102 18487 Z= 0.244 Angle : 0.659 9.421 25020 Z= 0.361 Chirality : 0.044 0.333 2793 Planarity : 0.004 0.068 3162 Dihedral : 18.538 165.883 7086 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.01 % Favored : 93.94 % Rotamer: Outliers : 4.33 % Allowed : 25.86 % Favored : 69.82 % 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: -1.90 (0.18), residues: 2195 helix: -0.78 (0.18), residues: 776 sheet: -1.56 (0.26), residues: 412 loop : -1.38 (0.19), residues: 1007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 675 HIS 0.004 0.001 HIS A 680 PHE 0.018 0.001 PHE F 543 TYR 0.020 0.001 TYR D 482 ARG 0.012 0.000 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 172 time to evaluate : 2.279 Fit side-chains REVERT: C 431 ASP cc_start: 0.8509 (t0) cc_final: 0.8287 (m-30) REVERT: F 547 MET cc_start: 0.6941 (mpt) cc_final: 0.6610 (mpt) outliers start: 87 outliers final: 74 residues processed: 251 average time/residue: 1.2194 time to fit residues: 344.6288 Evaluate side-chains 240 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 166 time to evaluate : 2.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 429 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 518 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 631 SER Chi-restraints excluded: chain C residue 634 SER Chi-restraints excluded: chain C residue 640 GLU Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 354 SER Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 556 SER Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 334 LEU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 370 SER Chi-restraints excluded: chain A residue 380 SER Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 436 TYR Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 518 SER Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 346 ASP Chi-restraints excluded: chain F residue 349 VAL Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 382 GLU Chi-restraints excluded: chain F residue 429 SER Chi-restraints excluded: chain F residue 455 SER Chi-restraints excluded: chain F residue 488 SER Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 558 LEU Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain F residue 674 LYS Chi-restraints excluded: chain E residue 331 GLN Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 455 SER Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 487 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 558 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 183 optimal weight: 5.9990 chunk 164 optimal weight: 20.0000 chunk 91 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 87 optimal weight: 0.8980 chunk 170 optimal weight: 20.0000 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 126 optimal weight: 0.9980 chunk 197 optimal weight: 5.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN A 324 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.0446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18487 Z= 0.317 Angle : 0.626 9.482 25020 Z= 0.319 Chirality : 0.045 0.158 2793 Planarity : 0.004 0.054 3162 Dihedral : 13.014 168.957 2666 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.33 % Favored : 93.62 % Rotamer: Outliers : 5.72 % Allowed : 24.22 % Favored : 70.06 % 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: -1.77 (0.18), residues: 2195 helix: -0.59 (0.19), residues: 767 sheet: -1.43 (0.26), residues: 393 loop : -1.42 (0.19), residues: 1035 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 355 HIS 0.005 0.001 HIS D 548 PHE 0.014 0.002 PHE D 524 TYR 0.020 0.001 TYR A 482 ARG 0.005 0.001 ARG F 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 172 time to evaluate : 2.139 Fit side-chains REVERT: C 592 ILE cc_start: 0.8882 (OUTLIER) cc_final: 0.8668 (pp) REVERT: B 554 PHE cc_start: 0.9170 (OUTLIER) cc_final: 0.8573 (t80) REVERT: A 617 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7198 (tp) REVERT: F 664 TYR cc_start: 0.4826 (m-80) cc_final: 0.4578 (m-10) outliers start: 115 outliers final: 64 residues processed: 269 average time/residue: 1.2453 time to fit residues: 376.7017 Evaluate side-chains 227 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 160 time to evaluate : 2.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 336 THR Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 478 ASN Chi-restraints excluded: chain A residue 497 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 346 ASP Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 631 SER Chi-restraints excluded: chain F residue 648 VAL Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 109 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 164 optimal weight: 20.0000 chunk 134 optimal weight: 9.9990 chunk 54 optimal weight: 0.9980 chunk 197 optimal weight: 4.9990 chunk 213 optimal weight: 9.9990 chunk 175 optimal weight: 4.9990 chunk 195 optimal weight: 5.9990 chunk 67 optimal weight: 0.5980 chunk 158 optimal weight: 1.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN A 324 ASN F 662 ASN E 660 GLN E 680 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.0607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18487 Z= 0.210 Angle : 0.568 8.505 25020 Z= 0.290 Chirality : 0.043 0.144 2793 Planarity : 0.004 0.045 3162 Dihedral : 12.403 170.325 2619 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.79 % Favored : 94.17 % Rotamer: Outliers : 5.17 % Allowed : 24.86 % Favored : 69.97 % 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: -1.58 (0.18), residues: 2195 helix: -0.43 (0.19), residues: 775 sheet: -1.29 (0.26), residues: 410 loop : -1.32 (0.19), residues: 1010 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 355 HIS 0.003 0.001 HIS D 548 PHE 0.012 0.001 PHE D 524 TYR 0.018 0.001 TYR B 482 ARG 0.005 0.000 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 169 time to evaluate : 1.738 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 554 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8608 (t80) REVERT: D 557 GLU cc_start: 0.6673 (OUTLIER) cc_final: 0.6193 (mp0) REVERT: A 581 CYS cc_start: 0.8191 (OUTLIER) cc_final: 0.7578 (t) REVERT: F 413 LEU cc_start: 0.7712 (OUTLIER) cc_final: 0.7407 (tm) REVERT: E 372 ARG cc_start: 0.8658 (OUTLIER) cc_final: 0.8273 (ttp-170) outliers start: 104 outliers final: 62 residues processed: 260 average time/residue: 1.3501 time to fit residues: 390.1229 Evaluate side-chains 230 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 163 time to evaluate : 1.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 518 SER Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 488 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 516 LEU Chi-restraints excluded: chain F residue 527 THR Chi-restraints excluded: chain F residue 547 MET Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 631 SER Chi-restraints excluded: chain E residue 372 ARG Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 471 LEU Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 543 PHE Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 195 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 132 optimal weight: 0.4980 chunk 198 optimal weight: 0.8980 chunk 209 optimal weight: 0.4980 chunk 103 optimal weight: 3.9990 chunk 187 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN A 324 ASN A 478 ASN F 662 ASN E 660 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18487 Z= 0.148 Angle : 0.532 8.678 25020 Z= 0.270 Chirality : 0.041 0.142 2793 Planarity : 0.004 0.050 3162 Dihedral : 11.817 171.060 2605 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 5.22 % Allowed : 25.16 % Favored : 69.62 % 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: -1.33 (0.18), residues: 2195 helix: -0.17 (0.19), residues: 778 sheet: -1.09 (0.28), residues: 386 loop : -1.27 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 675 HIS 0.002 0.001 HIS D 347 PHE 0.010 0.001 PHE D 524 TYR 0.015 0.001 TYR C 482 ARG 0.006 0.000 ARG F 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 186 time to evaluate : 2.345 Fit side-chains revert: symmetry clash REVERT: C 544 ILE cc_start: 0.9325 (OUTLIER) cc_final: 0.9070 (tp) REVERT: B 554 PHE cc_start: 0.9188 (OUTLIER) cc_final: 0.8675 (t80) REVERT: D 377 LYS cc_start: 0.8393 (mmtt) cc_final: 0.7988 (tptp) REVERT: D 557 GLU cc_start: 0.6683 (OUTLIER) cc_final: 0.6156 (mp0) REVERT: D 607 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8064 (mtmm) REVERT: A 617 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7026 (tp) REVERT: F 413 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7481 (tm) REVERT: F 649 LYS cc_start: 0.6075 (OUTLIER) cc_final: 0.5634 (mtpp) REVERT: E 663 ARG cc_start: 0.7524 (ttt90) cc_final: 0.7323 (ttt90) outliers start: 105 outliers final: 49 residues processed: 276 average time/residue: 1.4134 time to fit residues: 432.5955 Evaluate side-chains 218 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 162 time to evaluate : 2.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 380 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 648 VAL Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 174 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 3 optimal weight: 5.9990 chunk 156 optimal weight: 7.9990 chunk 86 optimal weight: 0.1980 chunk 178 optimal weight: 9.9990 chunk 144 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 188 optimal weight: 3.9990 chunk 52 optimal weight: 0.3980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN D 324 ASN D 478 ASN D 642 ASN A 324 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 ASN E 660 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 18487 Z= 0.276 Angle : 0.601 8.888 25020 Z= 0.304 Chirality : 0.044 0.144 2793 Planarity : 0.004 0.047 3162 Dihedral : 11.851 170.417 2591 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.10 % Favored : 93.85 % Rotamer: Outliers : 5.57 % Allowed : 24.91 % Favored : 69.52 % 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: -1.32 (0.18), residues: 2195 helix: -0.19 (0.19), residues: 767 sheet: -1.13 (0.27), residues: 400 loop : -1.20 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 355 HIS 0.005 0.001 HIS E 548 PHE 0.013 0.001 PHE F 444 TYR 0.029 0.002 TYR F 664 ARG 0.008 0.001 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 161 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: C 544 ILE cc_start: 0.9378 (OUTLIER) cc_final: 0.9115 (tp) REVERT: C 592 ILE cc_start: 0.8823 (OUTLIER) cc_final: 0.8613 (pp) REVERT: B 554 PHE cc_start: 0.9187 (OUTLIER) cc_final: 0.8605 (t80) REVERT: D 557 GLU cc_start: 0.6691 (OUTLIER) cc_final: 0.6151 (mp0) REVERT: D 607 LYS cc_start: 0.8408 (OUTLIER) cc_final: 0.8061 (mtmm) REVERT: A 581 CYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7927 (t) REVERT: A 617 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7153 (tp) REVERT: A 640 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.6439 (mp0) REVERT: F 375 LEU cc_start: 0.8777 (OUTLIER) cc_final: 0.8316 (mp) REVERT: F 413 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7497 (tm) REVERT: F 649 LYS cc_start: 0.6071 (OUTLIER) cc_final: 0.5604 (mtpp) REVERT: F 664 TYR cc_start: 0.4871 (m-10) cc_final: 0.4480 (m-80) outliers start: 112 outliers final: 70 residues processed: 253 average time/residue: 1.2363 time to fit residues: 351.9301 Evaluate side-chains 237 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 156 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 360 GLU Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 592 ILE Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 359 SER Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 365 THR Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 640 GLU Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 346 ASP Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 70 optimal weight: 0.6980 chunk 188 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 209 optimal weight: 0.0670 chunk 174 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN A 324 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 ASN E 660 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 18487 Z= 0.149 Angle : 0.534 9.494 25020 Z= 0.270 Chirality : 0.041 0.139 2793 Planarity : 0.004 0.046 3162 Dihedral : 11.535 170.795 2591 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 4.53 % Allowed : 26.16 % Favored : 69.32 % 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: -1.18 (0.18), residues: 2195 helix: -0.01 (0.19), residues: 776 sheet: -0.99 (0.27), residues: 396 loop : -1.23 (0.19), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 350 HIS 0.002 0.001 HIS D 347 PHE 0.010 0.001 PHE D 588 TYR 0.015 0.001 TYR C 482 ARG 0.007 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 168 time to evaluate : 2.052 Fit side-chains revert: symmetry clash REVERT: C 544 ILE cc_start: 0.9328 (OUTLIER) cc_final: 0.9088 (tp) REVERT: B 554 PHE cc_start: 0.9197 (OUTLIER) cc_final: 0.8685 (t80) REVERT: D 343 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.8048 (mm-30) REVERT: D 557 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: D 607 LYS cc_start: 0.8383 (OUTLIER) cc_final: 0.8036 (mtmm) REVERT: A 581 CYS cc_start: 0.8373 (OUTLIER) cc_final: 0.7799 (t) REVERT: A 617 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7107 (tp) REVERT: F 375 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8276 (mp) REVERT: F 413 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7482 (tm) REVERT: F 649 LYS cc_start: 0.6079 (OUTLIER) cc_final: 0.5605 (mtpp) outliers start: 91 outliers final: 53 residues processed: 244 average time/residue: 1.3211 time to fit residues: 364.4213 Evaluate side-chains 222 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 159 time to evaluate : 2.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 363 LEU Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 374 GLN Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 436 TYR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 202 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 119 optimal weight: 3.9990 chunk 153 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 176 optimal weight: 0.6980 chunk 117 optimal weight: 0.8980 chunk 209 optimal weight: 6.9990 chunk 130 optimal weight: 4.9990 chunk 127 optimal weight: 4.9990 chunk 96 optimal weight: 8.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN D 605 ASN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 548 HIS F 662 ASN E 660 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 18487 Z= 0.426 Angle : 0.685 9.765 25020 Z= 0.346 Chirality : 0.048 0.161 2793 Planarity : 0.005 0.066 3162 Dihedral : 11.987 170.239 2588 Min Nonbonded Distance : 1.795 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer: Outliers : 5.97 % Allowed : 24.71 % Favored : 69.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.18), residues: 2195 helix: -0.32 (0.19), residues: 764 sheet: -1.12 (0.26), residues: 417 loop : -1.24 (0.20), residues: 1014 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 355 HIS 0.007 0.002 HIS D 548 PHE 0.017 0.002 PHE C 444 TYR 0.024 0.002 TYR A 482 ARG 0.007 0.001 ARG F 612 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 160 time to evaluate : 2.118 Fit side-chains revert: symmetry clash REVERT: B 554 PHE cc_start: 0.9175 (OUTLIER) cc_final: 0.8576 (t80) REVERT: D 343 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: D 557 GLU cc_start: 0.6714 (OUTLIER) cc_final: 0.6200 (mp0) REVERT: D 572 ASP cc_start: 0.8636 (OUTLIER) cc_final: 0.8430 (p0) REVERT: D 607 LYS cc_start: 0.8432 (OUTLIER) cc_final: 0.8082 (mtmm) REVERT: A 617 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7197 (tp) REVERT: F 375 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8343 (mp) REVERT: F 413 LEU cc_start: 0.7754 (OUTLIER) cc_final: 0.7449 (tm) REVERT: F 649 LYS cc_start: 0.6145 (OUTLIER) cc_final: 0.5658 (mtpp) REVERT: E 387 ARG cc_start: 0.7290 (OUTLIER) cc_final: 0.6857 (ptt-90) outliers start: 120 outliers final: 80 residues processed: 261 average time/residue: 1.2746 time to fit residues: 372.7486 Evaluate side-chains 246 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 156 time to evaluate : 2.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 497 CYS Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 334 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 476 LYS Chi-restraints excluded: chain B residue 497 CYS Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 634 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 419 VAL Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 572 ASP Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 634 SER Chi-restraints excluded: chain D residue 681 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 338 SER Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 346 ASP Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 614 ASP Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 387 ARG Chi-restraints excluded: chain E residue 399 MET Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 530 THR Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 129 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 132 optimal weight: 0.5980 chunk 142 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 662 ASN E 660 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18487 Z= 0.206 Angle : 0.574 9.739 25020 Z= 0.292 Chirality : 0.043 0.146 2793 Planarity : 0.004 0.045 3162 Dihedral : 11.602 169.976 2583 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 5.02 % Allowed : 26.11 % Favored : 68.87 % 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: -1.30 (0.18), residues: 2195 helix: -0.15 (0.19), residues: 770 sheet: -1.09 (0.27), residues: 394 loop : -1.23 (0.19), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 355 HIS 0.003 0.001 HIS D 548 PHE 0.012 0.001 PHE D 524 TYR 0.017 0.001 TYR B 482 ARG 0.009 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 166 time to evaluate : 2.162 Fit side-chains revert: symmetry clash REVERT: C 544 ILE cc_start: 0.9365 (OUTLIER) cc_final: 0.9101 (tp) REVERT: B 554 PHE cc_start: 0.9196 (OUTLIER) cc_final: 0.8652 (t80) REVERT: D 343 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8066 (mm-30) REVERT: D 557 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6379 (mp0) REVERT: D 607 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8053 (mtmm) REVERT: A 581 CYS cc_start: 0.8385 (OUTLIER) cc_final: 0.7877 (t) REVERT: A 617 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7153 (tp) REVERT: F 375 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8279 (mp) REVERT: F 649 LYS cc_start: 0.6138 (OUTLIER) cc_final: 0.5657 (mtpp) outliers start: 101 outliers final: 65 residues processed: 248 average time/residue: 1.3226 time to fit residues: 367.0098 Evaluate side-chains 238 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 164 time to evaluate : 2.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 346 ASP Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 571 SER Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain C residue 649 LYS Chi-restraints excluded: chain B residue 346 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 631 SER Chi-restraints excluded: chain B residue 681 ILE Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 426 MET Chi-restraints excluded: chain D residue 449 THR Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 589 SER Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 334 LEU Chi-restraints excluded: chain F residue 339 VAL Chi-restraints excluded: chain F residue 346 ASP Chi-restraints excluded: chain F residue 372 ARG Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 599 THR Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 452 VAL Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 480 GLU Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 534 ASP Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 190 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 182 optimal weight: 0.2980 chunk 194 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 153 optimal weight: 3.9990 chunk 59 optimal weight: 0.0970 chunk 176 optimal weight: 3.9990 chunk 184 optimal weight: 0.8980 chunk 127 optimal weight: 0.0020 overall best weight: 0.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 18487 Z= 0.136 Angle : 0.542 10.577 25020 Z= 0.272 Chirality : 0.041 0.155 2793 Planarity : 0.004 0.046 3162 Dihedral : 11.174 170.923 2583 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 3.43 % Allowed : 27.65 % Favored : 68.92 % 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: -1.06 (0.18), residues: 2195 helix: 0.11 (0.19), residues: 774 sheet: -0.91 (0.29), residues: 365 loop : -1.19 (0.19), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 675 HIS 0.002 0.000 HIS D 347 PHE 0.010 0.001 PHE D 588 TYR 0.015 0.001 TYR C 482 ARG 0.010 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 173 time to evaluate : 2.240 Fit side-chains revert: symmetry clash REVERT: C 544 ILE cc_start: 0.9309 (OUTLIER) cc_final: 0.9078 (tp) REVERT: B 554 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8727 (t80) REVERT: D 343 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8026 (mm-30) REVERT: D 557 GLU cc_start: 0.6885 (OUTLIER) cc_final: 0.6388 (mp0) REVERT: D 607 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.8078 (mtmm) REVERT: A 617 LEU cc_start: 0.7446 (OUTLIER) cc_final: 0.7179 (tp) REVERT: F 375 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8213 (mp) REVERT: F 413 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7481 (tm) REVERT: F 649 LYS cc_start: 0.6175 (OUTLIER) cc_final: 0.5665 (mtpp) REVERT: E 631 SER cc_start: 0.6985 (OUTLIER) cc_final: 0.6579 (t) outliers start: 69 outliers final: 41 residues processed: 229 average time/residue: 1.3690 time to fit residues: 349.2711 Evaluate side-chains 215 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 164 time to evaluate : 2.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 571 SER Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 217 random chunks: chunk 206 optimal weight: 0.9990 chunk 125 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 143 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 172 optimal weight: 10.0000 chunk 17 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 105 optimal weight: 0.0030 chunk 136 optimal weight: 6.9990 overall best weight: 1.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 660 GLN B 529 GLN ** A 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 660 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 18487 Z= 0.224 Angle : 0.595 12.000 25020 Z= 0.298 Chirality : 0.043 0.140 2793 Planarity : 0.004 0.042 3162 Dihedral : 11.229 171.066 2575 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.43 % Allowed : 27.50 % Favored : 69.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.18), residues: 2195 helix: 0.05 (0.19), residues: 778 sheet: -0.98 (0.28), residues: 391 loop : -1.14 (0.19), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 675 HIS 0.004 0.001 HIS D 548 PHE 0.017 0.001 PHE F 444 TYR 0.019 0.001 TYR B 482 ARG 0.009 0.001 ARG E 663 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4390 Ramachandran restraints generated. 2195 Oldfield, 0 Emsley, 2195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 169 time to evaluate : 2.262 Fit side-chains revert: symmetry clash REVERT: C 544 ILE cc_start: 0.9363 (OUTLIER) cc_final: 0.9103 (tp) REVERT: B 554 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8674 (t80) REVERT: D 343 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: D 557 GLU cc_start: 0.6907 (OUTLIER) cc_final: 0.6424 (mp0) REVERT: D 607 LYS cc_start: 0.8405 (OUTLIER) cc_final: 0.8068 (mtmm) REVERT: A 617 LEU cc_start: 0.7526 (OUTLIER) cc_final: 0.7225 (tp) REVERT: F 375 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8223 (mp) REVERT: F 413 LEU cc_start: 0.7739 (OUTLIER) cc_final: 0.7499 (tm) REVERT: F 649 LYS cc_start: 0.6146 (OUTLIER) cc_final: 0.5723 (mtpp) outliers start: 69 outliers final: 47 residues processed: 227 average time/residue: 1.2630 time to fit residues: 321.3553 Evaluate side-chains 221 residues out of total 2011 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 165 time to evaluate : 2.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 332 ARG Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 359 SER Chi-restraints excluded: chain C residue 498 LEU Chi-restraints excluded: chain C residue 505 THR Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 572 ASP Chi-restraints excluded: chain B residue 554 PHE Chi-restraints excluded: chain B residue 572 ASP Chi-restraints excluded: chain B residue 581 CYS Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain D residue 343 GLU Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 359 SER Chi-restraints excluded: chain D residue 487 SER Chi-restraints excluded: chain D residue 525 VAL Chi-restraints excluded: chain D residue 557 GLU Chi-restraints excluded: chain D residue 566 SER Chi-restraints excluded: chain D residue 607 LYS Chi-restraints excluded: chain D residue 683 ILE Chi-restraints excluded: chain D residue 693 ILE Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 324 ASN Chi-restraints excluded: chain A residue 346 ASP Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 426 MET Chi-restraints excluded: chain A residue 499 THR Chi-restraints excluded: chain A residue 505 THR Chi-restraints excluded: chain A residue 525 VAL Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 617 LEU Chi-restraints excluded: chain A residue 624 VAL Chi-restraints excluded: chain A residue 660 GLN Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 689 THR Chi-restraints excluded: chain F residue 375 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 404 VAL Chi-restraints excluded: chain F residue 413 LEU Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 489 CYS Chi-restraints excluded: chain F residue 525 VAL Chi-restraints excluded: chain F residue 555 CYS Chi-restraints excluded: chain F residue 649 LYS Chi-restraints excluded: chain E residue 380 SER Chi-restraints excluded: chain E residue 408 THR Chi-restraints excluded: chain E residue 472 THR Chi-restraints excluded: chain E residue 488 SER Chi-restraints excluded: chain E residue 497 CYS Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 525 VAL Chi-restraints excluded: chain E residue 527 THR Chi-restraints excluded: chain E residue 544 ILE Chi-restraints excluded: chain E residue 558 LEU Chi-restraints excluded: chain E residue 571 SER Chi-restraints excluded: chain E residue 631 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/iotbx/cli_parser.py", line 944, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/programs/real_space_refine.py", line 189, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 700, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 764, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 71.6208 > 50: distance: 52 - 56: 34.667 distance: 53 - 80: 35.667 distance: 56 - 57: 39.075 distance: 57 - 60: 39.640 distance: 58 - 64: 40.419 distance: 59 - 89: 40.226 distance: 61 - 62: 39.880 distance: 61 - 63: 40.591 distance: 64 - 65: 40.057 distance: 67 - 98: 70.054 distance: 68 - 69: 40.671 distance: 69 - 70: 39.677 distance: 69 - 71: 39.502 distance: 73 - 74: 40.420 distance: 73 - 76: 39.159 distance: 74 - 75: 25.515 distance: 74 - 80: 40.119 distance: 76 - 77: 40.230 distance: 76 - 78: 40.294 distance: 77 - 79: 38.725 distance: 80 - 81: 12.341 distance: 81 - 82: 28.773 distance: 81 - 84: 10.003 distance: 82 - 83: 40.975 distance: 91 - 92: 38.981 distance: 93 - 94: 40.224 distance: 95 - 96: 40.031 distance: 100 - 101: 40.479 distance: 107 - 108: 40.463 distance: 108 - 109: 40.743 distance: 110 - 112: 39.511 distance: 115 - 116: 40.985 distance: 115 - 122: 56.025 distance: 118 - 119: 39.980 distance: 122 - 123: 40.610 distance: 122 - 128: 40.813 distance: 123 - 124: 40.535 distance: 126 - 127: 33.999 distance: 127 - 128: 33.077 distance: 129 - 130: 40.386 distance: 130 - 131: 37.778 distance: 131 - 135: 32.840