Starting phenix.real_space_refine on Sat Feb 17 11:11:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/02_2024/8hwf_35056_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/02_2024/8hwf_35056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/02_2024/8hwf_35056.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/02_2024/8hwf_35056.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/02_2024/8hwf_35056_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hwf_35056/02_2024/8hwf_35056_updated.pdb" } resolution = 3.3 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= 0.004 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 18 5.49 5 Mg 3 5.21 5 S 96 5.16 5 C 11684 2.51 5 N 3133 2.21 5 O 3507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 382": "OE1" <-> "OE2" Residue "C ASP 431": "OD1" <-> "OD2" Residue "C PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 459": "OE1" <-> "OE2" Residue "C TYR 482": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 504": "OE1" <-> "OE2" Residue "C PHE 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 610": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 656": "OD1" <-> "OD2" Residue "C PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 335": "OD1" <-> "OD2" Residue "B GLU 360": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 393": "OE1" <-> "OE2" Residue "B TYR 436": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 459": "OE1" <-> "OE2" Residue "B GLU 480": "OE1" <-> "OE2" Residue "B ASP 522": "OD1" <-> "OD2" Residue "B PHE 524": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 572": "OD1" <-> "OD2" Residue "B ASP 643": "OD1" <-> "OD2" Residue "F ASP 346": "OD1" <-> "OD2" Residue "F GLU 405": "OE1" <-> "OE2" Residue "F ASP 467": "OD1" <-> "OD2" Residue "F PHE 502": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 579": "OE1" <-> "OE2" Residue "F TYR 606": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 656": "OD1" <-> "OD2" Residue "F TYR 687": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 335": "OD1" <-> "OD2" Residue "E GLU 378": "OE1" <-> "OE2" Residue "E PHE 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 534": "OD1" <-> "OD2" Residue "E PHE 543": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 427": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 428": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 454": "OD1" <-> "OD2" Residue "D GLU 459": "OE1" <-> "OE2" Residue "D GLU 526": "OE1" <-> "OE2" Residue "D PHE 554": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 557": "OE1" <-> "OE2" Residue "D GLU 579": "OE1" <-> "OE2" Residue "D ASP 603": "OD1" <-> "OD2" Residue "D PHE 698": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 405": "OE1" <-> "OE2" Residue "A ASP 424": "OD1" <-> "OD2" Residue "A GLU 557": "OE1" <-> "OE2" Residue "A ASP 643": "OD1" <-> "OD2" Residue "A TYR 664": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18441 Number of models: 1 Model: "" Number of chains: 13 Chain: "C" 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: "B" 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: "F" Number of atoms: 2989 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2989 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 17, 'TRANS': 353} Chain: "E" Number of atoms: 2963 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2963 Classifications: {'peptide': 368} Link IDs: {'PTRANS': 17, 'TRANS': 350} 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: 3051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3051 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 18, 'TRANS': 359} 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: 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: "B" 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: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "A" 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: 9.98, per 1000 atoms: 0.54 Number of scatterers: 18441 At special positions: 0 Unit cell: (115.776, 122.208, 129.712, 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 96 16.00 P 18 15.00 Mg 3 11.99 O 3507 8.00 N 3133 7.00 C 11684 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: 6.74 Conformation dependent library (CDL) restraints added in 3.1 seconds 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4286 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 98 helices and 23 sheets defined 35.7% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.39 Creating SS restraints... Processing helix chain 'C' and resid 325 through 335 removed outlier: 3.653A pdb=" N ALA C 330 " --> pdb=" O LEU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 364 through 374 removed outlier: 3.567A pdb=" N ARG C 372 " --> pdb=" O ILE C 368 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N HIS C 373 " --> pdb=" O LEU C 369 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLN C 374 " --> pdb=" O SER C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 380 No H-bonds generated for 'chain 'C' and resid 377 through 380' Processing helix chain 'C' and resid 386 through 399 removed outlier: 3.543A pdb=" N THR C 391 " --> pdb=" O ARG C 387 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 433 Processing helix chain 'C' and resid 456 through 468 Processing helix chain 'C' and resid 477 through 490 removed outlier: 3.914A pdb=" N CYS C 489 " --> pdb=" O THR C 485 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU C 490 " --> pdb=" O LEU C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 520 Processing helix chain 'C' and resid 529 through 533 removed outlier: 3.776A pdb=" N THR C 533 " --> pdb=" O THR C 530 " (cutoff:3.500A) Processing helix chain 'C' and resid 542 through 547 removed outlier: 4.848A pdb=" N MET C 547 " --> pdb=" O PHE C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 578 removed outlier: 3.880A pdb=" N THR C 578 " --> pdb=" O ILE C 574 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 620 removed outlier: 4.309A pdb=" N ARG C 620 " --> pdb=" O ALA C 616 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 640 removed outlier: 3.853A pdb=" N GLU C 640 " --> pdb=" O ARG C 636 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 636 through 640' Processing helix chain 'C' and resid 657 through 660 No H-bonds generated for 'chain 'C' and resid 657 through 660' Processing helix chain 'C' and resid 666 through 679 Processing helix chain 'C' and resid 694 through 699 Processing helix chain 'B' and resid 325 through 336 Processing helix chain 'B' and resid 364 through 373 removed outlier: 3.745A pdb=" N ARG B 372 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N HIS B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 380 No H-bonds generated for 'chain 'B' and resid 377 through 380' Processing helix chain 'B' and resid 382 through 384 No H-bonds generated for 'chain 'B' and resid 382 through 384' Processing helix chain 'B' and resid 386 through 399 removed outlier: 4.089A pdb=" N THR B 391 " --> pdb=" O ARG B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 433 No H-bonds generated for 'chain 'B' and resid 431 through 433' Processing helix chain 'B' and resid 456 through 468 Processing helix chain 'B' and resid 477 through 490 removed outlier: 3.931A pdb=" N CYS B 489 " --> pdb=" O THR B 485 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N LEU B 490 " --> pdb=" O LEU B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 520 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 542 through 545 No H-bonds generated for 'chain 'B' and resid 542 through 545' Processing helix chain 'B' and resid 571 through 578 removed outlier: 3.721A pdb=" N LYS B 575 " --> pdb=" O SER B 571 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 620 removed outlier: 3.940A pdb=" N ARG B 619 " --> pdb=" O ASN B 615 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N ARG B 620 " --> pdb=" O ALA B 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 615 through 620' Processing helix chain 'B' and resid 637 through 640 Processing helix chain 'B' and resid 657 through 660 No H-bonds generated for 'chain 'B' and resid 657 through 660' Processing helix chain 'B' and resid 666 through 679 removed outlier: 3.662A pdb=" N LYS B 678 " --> pdb=" O LYS B 674 " (cutoff:3.500A) Processing helix chain 'B' and resid 690 through 692 No H-bonds generated for 'chain 'B' and resid 690 through 692' Processing helix chain 'B' and resid 694 through 699 Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.862A pdb=" N THR F 336 " --> pdb=" O ARG F 332 " (cutoff:3.500A) Processing helix chain 'F' and resid 364 through 374 removed outlier: 4.960A pdb=" N HIS F 373 " --> pdb=" O LEU F 369 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N GLN F 374 " --> pdb=" O SER F 370 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 380 No H-bonds generated for 'chain 'F' and resid 377 through 380' Processing helix chain 'F' and resid 386 through 399 Processing helix chain 'F' and resid 430 through 433 Processing helix chain 'F' and resid 448 through 450 No H-bonds generated for 'chain 'F' and resid 448 through 450' Processing helix chain 'F' and resid 456 through 468 Processing helix chain 'F' and resid 476 through 490 removed outlier: 3.941A pdb=" N CYS F 489 " --> pdb=" O THR F 485 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N LEU F 490 " --> pdb=" O LEU F 486 " (cutoff:3.500A) Processing helix chain 'F' and resid 509 through 519 Processing helix chain 'F' and resid 529 through 532 Processing helix chain 'F' and resid 542 through 545 No H-bonds generated for 'chain 'F' and resid 542 through 545' Processing helix chain 'F' and resid 571 through 577 Processing helix chain 'F' and resid 633 through 639 removed outlier: 5.005A pdb=" N GLU F 637 " --> pdb=" O SER F 634 " (cutoff:3.500A) Processing helix chain 'F' and resid 653 through 660 removed outlier: 3.547A pdb=" N LYS F 658 " --> pdb=" O GLY F 654 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ILE F 659 " --> pdb=" O LEU F 655 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLN F 660 " --> pdb=" O ASP F 656 " (cutoff:3.500A) Processing helix chain 'F' and resid 666 through 679 Processing helix chain 'E' and resid 325 through 336 removed outlier: 3.827A pdb=" N THR E 336 " --> pdb=" O ARG E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 364 through 374 removed outlier: 4.725A pdb=" N HIS E 373 " --> pdb=" O LEU E 369 " (cutoff:3.500A) removed outlier: 5.072A 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 386 through 399 Processing helix chain 'E' and resid 430 through 433 Processing helix chain 'E' and resid 456 through 468 Processing helix chain 'E' and resid 477 through 490 removed outlier: 3.624A pdb=" N CYS E 489 " --> pdb=" O THR E 485 " (cutoff:3.500A) removed outlier: 4.625A 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 532 Processing helix chain 'E' and resid 542 through 546 removed outlier: 4.342A pdb=" N ASN E 546 " --> pdb=" O PHE E 543 " (cutoff:3.500A) Processing helix chain 'E' and resid 571 through 576 Processing helix chain 'E' and resid 615 through 620 removed outlier: 3.653A pdb=" N ARG E 619 " --> pdb=" O ASN E 615 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N ARG E 620 " --> pdb=" O ALA E 616 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 615 through 620' Processing helix chain 'E' and resid 636 through 640 Processing helix chain 'E' and resid 657 through 660 No H-bonds generated for 'chain 'E' and resid 657 through 660' Processing helix chain 'E' and resid 666 through 679 Processing helix chain 'D' and resid 325 through 336 removed outlier: 3.585A pdb=" N ILE D 329 " --> pdb=" O LYS D 325 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA D 330 " --> pdb=" O LEU D 326 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 336 " --> pdb=" O ARG D 332 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 373 removed outlier: 3.815A pdb=" N ARG D 372 " --> pdb=" O ILE D 368 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N HIS D 373 " --> pdb=" O LEU D 369 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 380 No H-bonds generated for 'chain 'D' and resid 377 through 380' Processing helix chain 'D' and resid 386 through 398 removed outlier: 3.651A pdb=" N THR D 391 " --> pdb=" O ARG D 387 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 456 through 468 Processing helix chain 'D' and resid 473 through 475 No H-bonds generated for 'chain 'D' and resid 473 through 475' Processing helix chain 'D' and resid 477 through 490 removed outlier: 3.878A pdb=" N CYS D 489 " --> pdb=" O THR D 485 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N LEU D 490 " --> pdb=" O LEU D 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 509 through 520 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: 3.618A pdb=" N LEU D 577 " --> pdb=" O ASN D 573 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N THR D 578 " --> pdb=" O ILE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 618 through 620 No H-bonds generated for 'chain 'D' and resid 618 through 620' Processing helix chain 'D' and resid 636 through 641 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 694 through 699 Processing helix chain 'A' and resid 326 through 336 removed outlier: 3.902A 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 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 377 through 380 No H-bonds generated for 'chain 'A' and resid 377 through 380' Processing helix chain 'A' and resid 386 through 399 Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 456 through 468 Processing helix chain 'A' and resid 479 through 490 removed outlier: 3.945A pdb=" N CYS A 489 " --> pdb=" O THR A 485 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N LEU A 490 " --> pdb=" O LEU A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 523 removed outlier: 7.498A pdb=" N ASP A 522 " --> pdb=" O SER A 518 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 533 removed outlier: 3.529A 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 removed outlier: 3.813A pdb=" N LYS A 575 " --> pdb=" O SER A 571 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LYS A 576 " --> pdb=" O ASP A 572 " (cutoff:3.500A) No H-bonds generated for '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 634 through 640 removed outlier: 4.572A pdb=" N GLU A 637 " --> pdb=" O SER A 634 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 638 " --> pdb=" O GLY A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 661 removed outlier: 4.246A pdb=" N GLN A 660 " --> pdb=" O ASP A 656 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ASN A 661 " --> pdb=" O GLY A 657 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 656 through 661' Processing helix chain 'A' and resid 665 through 679 removed outlier: 3.758A pdb=" N LYS A 678 " --> pdb=" O LYS A 674 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N TYR A 679 " --> pdb=" O TRP A 675 " (cutoff:3.500A) Processing helix chain 'A' and resid 690 through 692 No H-bonds generated for 'chain 'A' and resid 690 through 692' Processing helix chain 'A' and resid 694 through 699 Processing sheet with id= A, first strand: chain 'C' and resid 412 through 415 removed outlier: 3.974A pdb=" N GLY C 418 " --> pdb=" O PHE C 415 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 621 through 626 removed outlier: 6.109A pdb=" N LEU C 498 " --> pdb=" O ALA C 622 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL C 624 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N PHE C 500 " --> pdb=" O VAL C 624 " (cutoff:3.500A) removed outlier: 7.276A pdb=" N PHE C 626 " --> pdb=" O PHE C 500 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N PHE C 502 " --> pdb=" O PHE C 626 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE C 600 " --> pdb=" O THR C 499 " (cutoff:3.500A) removed outlier: 7.607A pdb=" N PHE C 501 " --> pdb=" O ILE C 600 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N ILE C 602 " --> pdb=" O PHE C 501 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLY C 503 " --> pdb=" O ILE C 602 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 581 through 583 Processing sheet with id= D, first strand: chain 'C' and resid 628 through 631 removed outlier: 6.437A pdb=" N LYS C 647 " --> pdb=" O HIS C 629 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N SER C 631 " --> pdb=" O LYS C 647 " (cutoff:3.500A) removed outlier: 6.011A pdb=" N LYS C 649 " --> pdb=" O SER C 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 412 through 415 removed outlier: 3.961A pdb=" N GLY B 418 " --> pdb=" O PHE B 415 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 621 through 626 removed outlier: 6.090A pdb=" N LEU B 498 " --> pdb=" O ALA B 622 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N VAL B 624 " --> pdb=" O LEU B 498 " (cutoff:3.500A) removed outlier: 6.000A pdb=" N PHE B 500 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE B 626 " --> pdb=" O PHE B 500 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N PHE B 502 " --> pdb=" O PHE B 626 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 581 through 583 Processing sheet with id= H, first strand: chain 'B' and resid 628 through 631 removed outlier: 6.288A pdb=" N LYS B 647 " --> pdb=" O HIS B 629 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N SER B 631 " --> pdb=" O LYS B 647 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N LYS B 649 " --> pdb=" O SER B 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'F' and resid 339 through 341 Processing sheet with id= J, first strand: chain 'F' and resid 412 through 414 Processing sheet with id= K, first strand: chain 'F' and resid 621 through 626 removed outlier: 6.288A pdb=" N LEU F 498 " --> pdb=" O ALA F 622 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N VAL F 624 " --> pdb=" O LEU F 498 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N PHE F 500 " --> pdb=" O VAL F 624 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N PHE F 626 " --> pdb=" O PHE F 500 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N PHE F 502 " --> pdb=" O PHE F 626 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY F 503 " --> pdb=" O THR F 604 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N VAL F 525 " --> pdb=" O PHE F 554 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'F' and resid 581 through 583 Processing sheet with id= M, first strand: chain 'E' and resid 339 through 341 Processing sheet with id= N, first strand: chain 'E' and resid 412 through 415 removed outlier: 3.712A pdb=" N GLY E 418 " --> pdb=" O PHE E 415 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 621 through 626 removed outlier: 6.016A pdb=" N LEU E 498 " --> pdb=" O ALA E 622 " (cutoff:3.500A) removed outlier: 7.823A pdb=" N VAL E 624 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N PHE E 500 " --> pdb=" O VAL E 624 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N PHE E 626 " --> pdb=" O PHE E 500 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N PHE E 502 " --> pdb=" O PHE E 626 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ILE E 600 " --> pdb=" O THR E 499 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N PHE E 501 " --> pdb=" O ILE E 600 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE E 602 " --> pdb=" O PHE E 501 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N GLY E 503 " --> pdb=" O ILE E 602 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR E 604 " --> pdb=" O GLY E 503 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL E 525 " --> pdb=" O PHE E 554 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'E' and resid 581 through 583 Processing sheet with id= Q, first strand: chain 'E' and resid 628 through 631 removed outlier: 6.282A pdb=" N LYS E 647 " --> pdb=" O HIS E 629 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N SER E 631 " --> pdb=" O LYS E 647 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS E 649 " --> pdb=" O SER E 631 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'D' and resid 412 through 415 removed outlier: 3.818A pdb=" N GLY D 418 " --> pdb=" O PHE D 415 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'D' and resid 601 through 604 removed outlier: 6.450A pdb=" N THR D 499 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N THR D 604 " --> pdb=" O THR D 499 " (cutoff:3.500A) removed outlier: 5.894A pdb=" N PHE D 501 " --> pdb=" O THR D 604 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'D' and resid 581 through 583 Processing sheet with id= U, first strand: chain 'A' and resid 412 through 415 Processing sheet with id= V, first strand: chain 'A' and resid 498 through 503 Processing sheet with id= W, first strand: chain 'A' and resid 524 through 526 removed outlier: 6.408A pdb=" N SER A 552 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N THR A 599 " --> pdb=" O VAL A 553 " (cutoff:3.500A) No H-bonds generated for sheet with id= W 448 hydrogen bonds defined for protein. 1278 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: 5.18 Time building geometry restraints manager: 7.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4941 1.33 - 1.45: 3305 1.45 - 1.58: 10424 1.58 - 1.70: 29 1.70 - 1.82: 138 Bond restraints: 18837 Sorted by residual: bond pdb=" C SER F 455 " pdb=" N PRO F 456 " ideal model delta sigma weight residual 1.336 1.363 -0.027 1.20e-02 6.94e+03 5.08e+00 bond pdb=" N ASP E 534 " pdb=" CA ASP E 534 " ideal model delta sigma weight residual 1.455 1.484 -0.029 1.32e-02 5.74e+03 4.87e+00 bond pdb=" C PRO F 456 " pdb=" O PRO F 456 " ideal model delta sigma weight residual 1.237 1.211 0.026 1.20e-02 6.94e+03 4.71e+00 bond pdb=" N GLU E 526 " pdb=" CA GLU E 526 " ideal model delta sigma weight residual 1.459 1.486 -0.026 1.27e-02 6.20e+03 4.26e+00 bond pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.25e+00 ... (remaining 18832 not shown) Histogram of bond angle deviations from ideal: 98.91 - 106.33: 551 106.33 - 113.74: 10483 113.74 - 121.16: 9292 121.16 - 128.57: 5076 128.57 - 135.98: 93 Bond angle restraints: 25495 Sorted by residual: angle pdb=" N LEU D 532 " pdb=" CA LEU D 532 " pdb=" C LEU D 532 " ideal model delta sigma weight residual 114.75 108.27 6.48 1.26e+00 6.30e-01 2.65e+01 angle pdb=" N LYS E 434 " pdb=" CA LYS E 434 " pdb=" C LYS E 434 " ideal model delta sigma weight residual 114.62 108.76 5.86 1.14e+00 7.69e-01 2.64e+01 angle pdb=" N ILE B 371 " pdb=" CA ILE B 371 " pdb=" C ILE B 371 " ideal model delta sigma weight residual 112.98 107.84 5.14 1.25e+00 6.40e-01 1.69e+01 angle pdb=" CB MET F 458 " pdb=" CG MET F 458 " pdb=" SD MET F 458 " ideal model delta sigma weight residual 112.70 122.34 -9.64 3.00e+00 1.11e-01 1.03e+01 angle pdb=" C SER B 556 " pdb=" N GLU B 557 " pdb=" CA GLU B 557 " ideal model delta sigma weight residual 122.40 127.01 -4.61 1.45e+00 4.76e-01 1.01e+01 ... (remaining 25490 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.63: 10898 31.63 - 63.26: 545 63.26 - 94.89: 20 94.89 - 126.52: 0 126.52 - 158.15: 3 Dihedral angle restraints: 11466 sinusoidal: 4859 harmonic: 6607 Sorted by residual: dihedral pdb=" C2' ADP C1001 " pdb=" C1' ADP C1001 " pdb=" N9 ADP C1001 " pdb=" C4 ADP C1001 " ideal model delta sinusoidal sigma weight residual 91.55 -39.79 131.34 1 2.00e+01 2.50e-03 3.99e+01 dihedral pdb=" CA ILE D 531 " pdb=" C ILE D 531 " pdb=" N LEU D 532 " pdb=" CA LEU D 532 " ideal model delta harmonic sigma weight residual 180.00 160.08 19.92 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DT S 3 " pdb=" C3' DT S 3 " pdb=" O3' DT S 3 " pdb=" P DT S 4 " ideal model delta sinusoidal sigma weight residual 220.00 61.85 158.15 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 11463 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 2240 0.049 - 0.098: 500 0.098 - 0.147: 94 0.147 - 0.196: 1 0.196 - 0.245: 1 Chirality restraints: 2836 Sorted by residual: chirality pdb=" CG LEU F 671 " pdb=" CB LEU F 671 " pdb=" CD1 LEU F 671 " pdb=" CD2 LEU F 671 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU E 577 " pdb=" CB LEU E 577 " pdb=" CD1 LEU E 577 " pdb=" CD2 LEU E 577 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.71e-01 chirality pdb=" CA GLU B 557 " pdb=" N GLU B 557 " pdb=" C GLU B 557 " pdb=" CB GLU B 557 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 2833 not shown) Planarity restraints: 3229 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 361 " 0.056 5.00e-02 4.00e+02 8.45e-02 1.14e+01 pdb=" N PRO D 362 " -0.146 5.00e-02 4.00e+02 pdb=" CA PRO D 362 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO D 362 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU C 361 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.35e+00 pdb=" N PRO C 362 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO C 362 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 362 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 522 " 0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" C ASP A 522 " -0.027 2.00e-02 2.50e+03 pdb=" O ASP A 522 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 523 " 0.009 2.00e-02 2.50e+03 ... (remaining 3226 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 219 2.61 - 3.18: 15590 3.18 - 3.76: 27626 3.76 - 4.33: 39705 4.33 - 4.90: 65646 Nonbonded interactions: 148786 Sorted by model distance: nonbonded pdb=" O3B ADP B1001 " pdb="MG MG B1002 " model vdw 2.039 2.170 nonbonded pdb=" OG SER B 510 " pdb="MG MG B1002 " model vdw 2.056 2.170 nonbonded pdb=" OG SER A 510 " pdb="MG MG A1002 " model vdw 2.069 2.170 nonbonded pdb=" OG SER C 510 " pdb="MG MG C1002 " model vdw 2.108 2.170 nonbonded pdb=" O2B ADP C1001 " pdb="MG MG C1002 " model vdw 2.183 2.170 ... (remaining 148781 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 690) selection = (chain 'B' and resid 323 through 690) selection = (chain 'C' and resid 323 through 690) selection = (chain 'D' and resid 323 through 690) selection = (chain 'E' and resid 323 through 690) selection = (chain 'F' and resid 323 through 690) } 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: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.810 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 47.840 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 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 : 0.003 0.045 18837 Z= 0.172 Angle : 0.656 10.128 25495 Z= 0.347 Chirality : 0.041 0.245 2836 Planarity : 0.003 0.085 3229 Dihedral : 17.293 158.154 7180 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 0.15 % Allowed : 25.77 % Favored : 74.08 % 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: -1.24 (0.18), residues: 2239 helix: 0.56 (0.21), residues: 697 sheet: -1.65 (0.30), residues: 319 loop : -1.42 (0.17), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 350 HIS 0.004 0.000 HIS F 629 PHE 0.016 0.001 PHE C 588 TYR 0.018 0.001 TYR E 482 ARG 0.007 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 236 time to evaluate : 2.125 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 387 ARG cc_start: 0.8387 (ptt90) cc_final: 0.8149 (ptt-90) REVERT: C 618 MET cc_start: 0.8642 (mtm) cc_final: 0.8248 (mmm) REVERT: F 618 MET cc_start: 0.8414 (mtm) cc_final: 0.8172 (mmp) REVERT: F 684 MET cc_start: 0.6667 (tmm) cc_final: 0.6461 (tmm) REVERT: E 578 THR cc_start: 0.8001 (m) cc_final: 0.7709 (p) REVERT: D 361 GLU cc_start: 0.8478 (pm20) cc_final: 0.8267 (pm20) REVERT: D 374 GLN cc_start: 0.8829 (mt0) cc_final: 0.8574 (mt0) REVERT: A 612 ARG cc_start: 0.8598 (mtm110) cc_final: 0.7475 (ptp90) outliers start: 3 outliers final: 1 residues processed: 237 average time/residue: 0.3202 time to fit residues: 113.3339 Evaluate side-chains 209 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 208 time to evaluate : 2.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 571 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 173 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 200 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 352 ASN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 590 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18837 Z= 0.181 Angle : 0.550 6.841 25495 Z= 0.264 Chirality : 0.041 0.161 2836 Planarity : 0.003 0.062 3229 Dihedral : 9.224 158.484 2565 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.59 % Allowed : 24.40 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.18), residues: 2239 helix: 0.89 (0.21), residues: 698 sheet: -1.60 (0.29), residues: 331 loop : -1.23 (0.18), residues: 1210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 350 HIS 0.002 0.001 HIS C 680 PHE 0.010 0.001 PHE F 630 TYR 0.016 0.001 TYR E 482 ARG 0.005 0.000 ARG D 570 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 217 time to evaluate : 2.343 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 387 ARG cc_start: 0.8443 (ptt90) cc_final: 0.8195 (ptt-90) REVERT: C 649 LYS cc_start: 0.8208 (tmtt) cc_final: 0.7998 (tmtt) REVERT: F 618 MET cc_start: 0.8476 (mtm) cc_final: 0.8100 (mmp) REVERT: E 578 THR cc_start: 0.8089 (m) cc_final: 0.7859 (p) REVERT: E 579 GLU cc_start: 0.7823 (mp0) cc_final: 0.7554 (mp0) REVERT: A 334 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8815 (mt) REVERT: A 344 ARG cc_start: 0.9239 (OUTLIER) cc_final: 0.7319 (ttp-170) REVERT: A 399 MET cc_start: 0.8533 (mtt) cc_final: 0.8314 (mtt) REVERT: A 522 ASP cc_start: 0.7952 (t0) cc_final: 0.7730 (t0) outliers start: 53 outliers final: 33 residues processed: 255 average time/residue: 0.3284 time to fit residues: 125.2630 Evaluate side-chains 241 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 111 optimal weight: 7.9990 chunk 62 optimal weight: 1.9990 chunk 167 optimal weight: 5.9990 chunk 136 optimal weight: 0.0010 chunk 55 optimal weight: 6.9990 chunk 201 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 chunk 179 optimal weight: 9.9990 chunk 199 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 161 optimal weight: 2.9990 overall best weight: 1.6992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 478 ASN ** E 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 18837 Z= 0.223 Angle : 0.563 9.140 25495 Z= 0.269 Chirality : 0.041 0.151 2836 Planarity : 0.003 0.053 3229 Dihedral : 9.171 158.544 2564 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.56 % Allowed : 23.91 % Favored : 72.52 % 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: -0.83 (0.18), residues: 2239 helix: 0.97 (0.20), residues: 700 sheet: -1.50 (0.29), residues: 341 loop : -1.18 (0.18), residues: 1198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 350 HIS 0.003 0.001 HIS D 680 PHE 0.010 0.001 PHE C 444 TYR 0.018 0.001 TYR E 482 ARG 0.004 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 216 time to evaluate : 2.423 Fit side-chains revert: symmetry clash REVERT: C 387 ARG cc_start: 0.8439 (ptt90) cc_final: 0.8178 (ptt-90) REVERT: C 455 SER cc_start: 0.8535 (OUTLIER) cc_final: 0.8227 (m) REVERT: C 615 ASN cc_start: 0.8403 (OUTLIER) cc_final: 0.8010 (m110) REVERT: C 649 LYS cc_start: 0.8382 (tmtt) cc_final: 0.8172 (tmtt) REVERT: F 618 MET cc_start: 0.8455 (mtm) cc_final: 0.8132 (mmp) REVERT: E 344 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7283 (tpp80) REVERT: E 576 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8446 (mmtt) REVERT: E 578 THR cc_start: 0.8201 (m) cc_final: 0.7752 (p) REVERT: D 365 THR cc_start: 0.9144 (OUTLIER) cc_final: 0.8913 (m) REVERT: D 614 ASP cc_start: 0.8600 (p0) cc_final: 0.8396 (p0) REVERT: A 334 LEU cc_start: 0.9244 (OUTLIER) cc_final: 0.8781 (mt) REVERT: A 344 ARG cc_start: 0.9229 (OUTLIER) cc_final: 0.7430 (ttp-170) REVERT: A 399 MET cc_start: 0.8594 (mtt) cc_final: 0.8259 (mtt) REVERT: A 522 ASP cc_start: 0.8115 (t0) cc_final: 0.7904 (t0) REVERT: A 681 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8125 (mm) outliers start: 73 outliers final: 44 residues processed: 273 average time/residue: 0.3221 time to fit residues: 133.5338 Evaluate side-chains 255 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 205 time to evaluate : 2.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 198 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 104 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 135 optimal weight: 9.9990 chunk 201 optimal weight: 2.9990 chunk 213 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 374 GLN ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 615 ASN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 18837 Z= 0.317 Angle : 0.598 8.226 25495 Z= 0.289 Chirality : 0.043 0.166 2836 Planarity : 0.003 0.047 3229 Dihedral : 9.241 158.597 2564 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 7.01 % Favored : 92.94 % Rotamer: Outliers : 4.15 % Allowed : 24.16 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.18), residues: 2239 helix: 0.68 (0.20), residues: 725 sheet: -1.21 (0.31), residues: 300 loop : -1.29 (0.17), residues: 1214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 350 HIS 0.005 0.001 HIS D 680 PHE 0.014 0.001 PHE F 630 TYR 0.019 0.001 TYR B 482 ARG 0.005 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 215 time to evaluate : 2.186 Fit side-chains revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8166 (m-30) cc_final: 0.7940 (m-30) REVERT: C 615 ASN cc_start: 0.8333 (OUTLIER) cc_final: 0.7928 (m110) REVERT: F 618 MET cc_start: 0.8395 (mtm) cc_final: 0.8085 (mmp) REVERT: E 344 ARG cc_start: 0.7656 (tpp80) cc_final: 0.7307 (tpp80) REVERT: E 576 LYS cc_start: 0.8826 (mmmt) cc_final: 0.8431 (mptt) REVERT: E 578 THR cc_start: 0.8307 (OUTLIER) cc_final: 0.7918 (p) REVERT: E 579 GLU cc_start: 0.7912 (mp0) cc_final: 0.7664 (mp0) REVERT: D 365 THR cc_start: 0.9170 (OUTLIER) cc_final: 0.8934 (m) REVERT: D 538 LYS cc_start: 0.8390 (pttp) cc_final: 0.8177 (pptt) REVERT: D 611 ASP cc_start: 0.8493 (m-30) cc_final: 0.8253 (m-30) REVERT: D 614 ASP cc_start: 0.8562 (p0) cc_final: 0.8352 (p0) REVERT: A 344 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.7441 (ttp-170) REVERT: A 522 ASP cc_start: 0.8351 (t0) cc_final: 0.8078 (t0) REVERT: A 681 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8146 (mm) outliers start: 85 outliers final: 64 residues processed: 281 average time/residue: 0.3255 time to fit residues: 135.6809 Evaluate side-chains 276 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 207 time to evaluate : 2.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 372 ARG Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 614 ASP Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 471 LEU Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 491 CYS Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 533 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 655 LEU Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain E residue 324 ASN Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 609 VAL Chi-restraints excluded: chain E residue 656 ASP Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 529 GLN Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 424 ASP Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 177 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 chunk 3 optimal weight: 0.0970 chunk 159 optimal weight: 0.2980 chunk 88 optimal weight: 10.0000 chunk 182 optimal weight: 3.9990 chunk 147 optimal weight: 0.1980 chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 478 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 629 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 moved from start: 0.0949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 18837 Z= 0.135 Angle : 0.538 8.074 25495 Z= 0.256 Chirality : 0.040 0.160 2836 Planarity : 0.003 0.041 3229 Dihedral : 9.014 159.973 2564 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 2.73 % Allowed : 26.11 % Favored : 71.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.18), residues: 2239 helix: 1.19 (0.21), residues: 705 sheet: -1.39 (0.29), residues: 341 loop : -1.05 (0.18), residues: 1193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 350 HIS 0.002 0.000 HIS F 629 PHE 0.008 0.001 PHE E 327 TYR 0.014 0.001 TYR E 482 ARG 0.011 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 231 time to evaluate : 2.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 335 ASP cc_start: 0.8169 (m-30) cc_final: 0.7951 (m-30) REVERT: F 387 ARG cc_start: 0.7643 (ptt-90) cc_final: 0.7385 (mpp-170) REVERT: F 618 MET cc_start: 0.8378 (mtm) cc_final: 0.8055 (mmp) REVERT: F 684 MET cc_start: 0.6686 (tmm) cc_final: 0.6480 (tmm) REVERT: E 575 LYS cc_start: 0.9248 (mttt) cc_final: 0.8769 (mtpt) REVERT: E 578 THR cc_start: 0.8240 (OUTLIER) cc_final: 0.7779 (p) REVERT: E 579 GLU cc_start: 0.7917 (mp0) cc_final: 0.7645 (mp0) REVERT: D 365 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8855 (m) REVERT: D 572 ASP cc_start: 0.8730 (p0) cc_final: 0.8506 (t0) REVERT: D 611 ASP cc_start: 0.8456 (m-30) cc_final: 0.8240 (m-30) REVERT: D 614 ASP cc_start: 0.8563 (p0) cc_final: 0.8332 (p0) REVERT: A 334 LEU cc_start: 0.9239 (OUTLIER) cc_final: 0.8814 (mt) REVERT: A 522 ASP cc_start: 0.8276 (t0) cc_final: 0.7900 (t0) REVERT: A 570 ARG cc_start: 0.8464 (mtp85) cc_final: 0.8118 (mtp180) REVERT: A 660 GLN cc_start: 0.8600 (mp10) cc_final: 0.8399 (mp10) outliers start: 56 outliers final: 35 residues processed: 272 average time/residue: 0.3341 time to fit residues: 136.7500 Evaluate side-chains 253 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 215 time to evaluate : 2.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 611 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 671 LEU Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 71 optimal weight: 0.8980 chunk 192 optimal weight: 5.9990 chunk 42 optimal weight: 0.2980 chunk 125 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 213 optimal weight: 7.9990 chunk 177 optimal weight: 0.7980 chunk 99 optimal weight: 10.0000 chunk 17 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 478 ASN ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 18837 Z= 0.196 Angle : 0.558 7.253 25495 Z= 0.267 Chirality : 0.041 0.165 2836 Planarity : 0.003 0.038 3229 Dihedral : 8.994 159.603 2564 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 3.42 % Allowed : 25.52 % Favored : 71.06 % 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: -0.57 (0.18), residues: 2239 helix: 1.19 (0.20), residues: 707 sheet: -1.38 (0.29), residues: 356 loop : -1.02 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 350 HIS 0.003 0.001 HIS D 680 PHE 0.008 0.001 PHE F 630 TYR 0.016 0.001 TYR B 482 ARG 0.007 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 218 time to evaluate : 1.976 Fit side-chains REVERT: C 335 ASP cc_start: 0.8179 (m-30) cc_final: 0.7959 (m-30) REVERT: F 387 ARG cc_start: 0.7681 (OUTLIER) cc_final: 0.7436 (mpp-170) REVERT: F 618 MET cc_start: 0.8366 (mtm) cc_final: 0.8047 (mmp) REVERT: F 684 MET cc_start: 0.6752 (OUTLIER) cc_final: 0.6543 (tmm) REVERT: E 570 ARG cc_start: 0.5780 (mtp85) cc_final: 0.5468 (mtm180) REVERT: E 575 LYS cc_start: 0.9223 (mttt) cc_final: 0.8751 (mtpt) REVERT: E 576 LYS cc_start: 0.8703 (mmmt) cc_final: 0.8345 (mptt) REVERT: E 578 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.7781 (p) REVERT: E 579 GLU cc_start: 0.7951 (mp0) cc_final: 0.7656 (mp0) REVERT: D 365 THR cc_start: 0.9089 (OUTLIER) cc_final: 0.8859 (m) REVERT: D 611 ASP cc_start: 0.8477 (m-30) cc_final: 0.8249 (m-30) REVERT: D 614 ASP cc_start: 0.8569 (p0) cc_final: 0.8328 (p0) REVERT: A 334 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8774 (mt) REVERT: A 344 ARG cc_start: 0.9186 (OUTLIER) cc_final: 0.7527 (ttp-170) REVERT: A 399 MET cc_start: 0.8503 (mtt) cc_final: 0.8135 (mtt) REVERT: A 522 ASP cc_start: 0.8347 (t0) cc_final: 0.7935 (t0) REVERT: A 579 GLU cc_start: 0.8010 (tm-30) cc_final: 0.7371 (tm-30) REVERT: A 611 ASP cc_start: 0.8865 (t70) cc_final: 0.8532 (p0) REVERT: A 660 GLN cc_start: 0.8598 (mp10) cc_final: 0.8105 (mp10) REVERT: A 684 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8537 (ttp) outliers start: 70 outliers final: 50 residues processed: 270 average time/residue: 0.3033 time to fit residues: 123.1618 Evaluate side-chains 267 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 210 time to evaluate : 2.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 611 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 507 THR Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain F residue 684 MET Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 578 THR Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 594 ASN Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 206 optimal weight: 6.9990 chunk 24 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 156 optimal weight: 3.9990 chunk 120 optimal weight: 0.9980 chunk 179 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 213 optimal weight: 0.3980 chunk 133 optimal weight: 3.9990 chunk 129 optimal weight: 0.9980 chunk 98 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18837 Z= 0.264 Angle : 0.596 9.727 25495 Z= 0.286 Chirality : 0.042 0.172 2836 Planarity : 0.003 0.036 3229 Dihedral : 9.071 159.592 2564 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.90 % Favored : 94.06 % Rotamer: Outliers : 3.32 % Allowed : 26.01 % Favored : 70.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.60 (0.18), residues: 2239 helix: 1.11 (0.20), residues: 709 sheet: -1.08 (0.31), residues: 311 loop : -1.12 (0.18), residues: 1219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 350 HIS 0.005 0.001 HIS D 680 PHE 0.011 0.001 PHE C 444 TYR 0.018 0.001 TYR B 482 ARG 0.005 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 219 time to evaluate : 2.142 Fit side-chains REVERT: C 335 ASP cc_start: 0.8177 (m-30) cc_final: 0.7955 (m-30) REVERT: C 382 GLU cc_start: 0.8513 (mt-10) cc_final: 0.8196 (mt-10) REVERT: C 615 ASN cc_start: 0.8503 (OUTLIER) cc_final: 0.8084 (m110) REVERT: F 387 ARG cc_start: 0.7712 (OUTLIER) cc_final: 0.7435 (mpp-170) REVERT: F 569 ILE cc_start: 0.7630 (mt) cc_final: 0.7313 (mm) REVERT: F 618 MET cc_start: 0.8365 (mtm) cc_final: 0.8035 (mmp) REVERT: E 570 ARG cc_start: 0.5779 (mtp85) cc_final: 0.5534 (mtm180) REVERT: E 575 LYS cc_start: 0.9220 (mttt) cc_final: 0.8821 (mtpt) REVERT: E 576 LYS cc_start: 0.8732 (mmmt) cc_final: 0.8450 (mptt) REVERT: E 578 THR cc_start: 0.8381 (m) cc_final: 0.7828 (p) REVERT: E 579 GLU cc_start: 0.8041 (mp0) cc_final: 0.7750 (mp0) REVERT: D 365 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8876 (m) REVERT: D 538 LYS cc_start: 0.8480 (pptt) cc_final: 0.7982 (pttp) REVERT: D 614 ASP cc_start: 0.8566 (p0) cc_final: 0.8320 (p0) REVERT: A 334 LEU cc_start: 0.9236 (OUTLIER) cc_final: 0.8763 (mt) REVERT: A 344 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.7440 (ttp-170) REVERT: A 399 MET cc_start: 0.8534 (mtt) cc_final: 0.8164 (mtt) REVERT: A 522 ASP cc_start: 0.8375 (t0) cc_final: 0.7943 (t0) REVERT: A 579 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7471 (tm-30) REVERT: A 660 GLN cc_start: 0.8559 (mp10) cc_final: 0.8053 (mp10) REVERT: A 684 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8554 (ttp) outliers start: 68 outliers final: 55 residues processed: 273 average time/residue: 0.3199 time to fit residues: 130.3615 Evaluate side-chains 274 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 213 time to evaluate : 2.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 611 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 131 optimal weight: 4.9990 chunk 85 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 41 optimal weight: 0.0670 chunk 135 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 193 optimal weight: 1.9990 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18837 Z= 0.218 Angle : 0.579 8.782 25495 Z= 0.277 Chirality : 0.041 0.156 2836 Planarity : 0.003 0.036 3229 Dihedral : 9.034 159.983 2564 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.42 % Allowed : 25.96 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.18), residues: 2239 helix: 1.19 (0.20), residues: 706 sheet: -1.18 (0.30), residues: 324 loop : -1.04 (0.18), residues: 1209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 350 HIS 0.003 0.001 HIS D 680 PHE 0.009 0.001 PHE C 444 TYR 0.017 0.001 TYR E 482 ARG 0.004 0.000 ARG A 612 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 215 time to evaluate : 2.157 Fit side-chains REVERT: C 335 ASP cc_start: 0.8175 (m-30) cc_final: 0.7948 (m-30) REVERT: C 382 GLU cc_start: 0.8488 (mt-10) cc_final: 0.8221 (mt-10) REVERT: C 455 SER cc_start: 0.8657 (OUTLIER) cc_final: 0.8377 (m) REVERT: F 387 ARG cc_start: 0.7682 (OUTLIER) cc_final: 0.6964 (ptt-90) REVERT: F 462 MET cc_start: 0.8567 (tpt) cc_final: 0.8151 (tpp) REVERT: F 505 THR cc_start: 0.8500 (m) cc_final: 0.8268 (p) REVERT: F 569 ILE cc_start: 0.7686 (mt) cc_final: 0.7360 (mm) REVERT: F 618 MET cc_start: 0.8388 (mtm) cc_final: 0.8049 (mmp) REVERT: E 570 ARG cc_start: 0.5810 (mtp85) cc_final: 0.5575 (mtm180) REVERT: E 575 LYS cc_start: 0.9215 (mttt) cc_final: 0.8888 (mtpt) REVERT: E 576 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8487 (mptt) REVERT: D 365 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8869 (m) REVERT: D 538 LYS cc_start: 0.8516 (pptt) cc_final: 0.7997 (pttp) REVERT: D 573 ASN cc_start: 0.9233 (t0) cc_final: 0.8920 (m-40) REVERT: D 579 GLU cc_start: 0.8697 (mp0) cc_final: 0.8056 (mp0) REVERT: D 614 ASP cc_start: 0.8557 (p0) cc_final: 0.8296 (p0) REVERT: A 334 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8802 (mt) REVERT: A 344 ARG cc_start: 0.9194 (OUTLIER) cc_final: 0.7560 (ttp-170) REVERT: A 399 MET cc_start: 0.8519 (mtt) cc_final: 0.8245 (mtt) REVERT: A 522 ASP cc_start: 0.8380 (t0) cc_final: 0.7954 (t0) REVERT: A 579 GLU cc_start: 0.8057 (tm-30) cc_final: 0.7454 (tm-30) REVERT: A 660 GLN cc_start: 0.8593 (mp10) cc_final: 0.8081 (mp10) REVERT: A 684 MET cc_start: 0.9149 (OUTLIER) cc_final: 0.8547 (ttp) outliers start: 70 outliers final: 56 residues processed: 268 average time/residue: 0.3085 time to fit residues: 123.9805 Evaluate side-chains 271 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 209 time to evaluate : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 611 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 204 optimal weight: 0.5980 chunk 186 optimal weight: 3.9990 chunk 198 optimal weight: 0.3980 chunk 119 optimal weight: 7.9990 chunk 86 optimal weight: 3.9990 chunk 155 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 187 optimal weight: 4.9990 chunk 197 optimal weight: 3.9990 chunk 130 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18837 Z= 0.277 Angle : 0.607 9.363 25495 Z= 0.291 Chirality : 0.042 0.151 2836 Planarity : 0.003 0.035 3229 Dihedral : 9.106 160.095 2564 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.43 % Favored : 93.52 % Rotamer: Outliers : 3.56 % Allowed : 25.87 % Favored : 70.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.18), residues: 2239 helix: 1.12 (0.20), residues: 707 sheet: -1.00 (0.31), residues: 310 loop : -1.11 (0.18), residues: 1222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 675 HIS 0.005 0.001 HIS D 680 PHE 0.012 0.001 PHE C 444 TYR 0.019 0.001 TYR B 482 ARG 0.005 0.000 ARG C 387 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 213 time to evaluate : 2.230 Fit side-chains REVERT: C 335 ASP cc_start: 0.8171 (m-30) cc_final: 0.7949 (m-30) REVERT: C 382 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8203 (mt-10) REVERT: C 455 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8412 (m) REVERT: C 615 ASN cc_start: 0.8525 (OUTLIER) cc_final: 0.8098 (m110) REVERT: F 387 ARG cc_start: 0.7739 (OUTLIER) cc_final: 0.7455 (mpp-170) REVERT: F 462 MET cc_start: 0.8588 (tpt) cc_final: 0.8181 (tpp) REVERT: F 505 THR cc_start: 0.8493 (m) cc_final: 0.8248 (p) REVERT: F 569 ILE cc_start: 0.7719 (mt) cc_final: 0.7448 (mm) REVERT: F 618 MET cc_start: 0.8401 (mtm) cc_final: 0.7992 (mmp) REVERT: E 575 LYS cc_start: 0.9172 (mttt) cc_final: 0.8874 (mtpt) REVERT: E 576 LYS cc_start: 0.8728 (mmmt) cc_final: 0.8424 (mptt) REVERT: D 365 THR cc_start: 0.9122 (OUTLIER) cc_final: 0.8875 (m) REVERT: D 538 LYS cc_start: 0.8502 (pptt) cc_final: 0.7974 (pttp) REVERT: D 579 GLU cc_start: 0.8672 (mp0) cc_final: 0.8015 (mp0) REVERT: D 614 ASP cc_start: 0.8571 (p0) cc_final: 0.8259 (p0) REVERT: A 334 LEU cc_start: 0.9235 (OUTLIER) cc_final: 0.8780 (mt) REVERT: A 344 ARG cc_start: 0.9217 (OUTLIER) cc_final: 0.7463 (ttp-170) REVERT: A 399 MET cc_start: 0.8561 (mtt) cc_final: 0.8191 (mtt) REVERT: A 522 ASP cc_start: 0.8397 (t0) cc_final: 0.7968 (t0) REVERT: A 579 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7465 (tm-30) REVERT: A 660 GLN cc_start: 0.8582 (mp10) cc_final: 0.8043 (mp10) REVERT: A 681 ILE cc_start: 0.8439 (OUTLIER) cc_final: 0.8132 (mm) REVERT: A 684 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8551 (ttp) outliers start: 73 outliers final: 60 residues processed: 269 average time/residue: 0.3195 time to fit residues: 130.3032 Evaluate side-chains 278 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 210 time to evaluate : 2.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 615 ASN Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain B residue 689 THR Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 387 ARG Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 582 VAL Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 507 THR Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 209 optimal weight: 1.9990 chunk 128 optimal weight: 9.9990 chunk 99 optimal weight: 5.9990 chunk 145 optimal weight: 8.9990 chunk 220 optimal weight: 4.9990 chunk 202 optimal weight: 0.9990 chunk 175 optimal weight: 6.9990 chunk 18 optimal weight: 0.0980 chunk 135 optimal weight: 0.2980 chunk 107 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 18837 Z= 0.190 Angle : 0.582 8.536 25495 Z= 0.278 Chirality : 0.041 0.266 2836 Planarity : 0.003 0.035 3229 Dihedral : 9.019 160.411 2564 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.32 % Allowed : 25.96 % Favored : 70.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.18), residues: 2239 helix: 1.28 (0.20), residues: 706 sheet: -0.92 (0.31), residues: 310 loop : -1.04 (0.18), residues: 1223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 675 HIS 0.003 0.000 HIS F 629 PHE 0.009 0.001 PHE C 502 TYR 0.016 0.001 TYR E 482 ARG 0.006 0.000 ARG C 387 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4478 Ramachandran restraints generated. 2239 Oldfield, 0 Emsley, 2239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 212 time to evaluate : 2.309 Fit side-chains REVERT: C 335 ASP cc_start: 0.8174 (m-30) cc_final: 0.7949 (m-30) REVERT: C 382 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8205 (mt-10) REVERT: C 455 SER cc_start: 0.8611 (OUTLIER) cc_final: 0.8392 (m) REVERT: F 462 MET cc_start: 0.8581 (tpt) cc_final: 0.8167 (tpp) REVERT: F 505 THR cc_start: 0.8609 (m) cc_final: 0.8384 (p) REVERT: F 618 MET cc_start: 0.8377 (mtm) cc_final: 0.7988 (mmp) REVERT: E 575 LYS cc_start: 0.9216 (mttt) cc_final: 0.8960 (mtpt) REVERT: E 576 LYS cc_start: 0.8731 (mmmt) cc_final: 0.8502 (mptt) REVERT: D 365 THR cc_start: 0.9096 (OUTLIER) cc_final: 0.8853 (m) REVERT: D 538 LYS cc_start: 0.8456 (pptt) cc_final: 0.7934 (pttp) REVERT: D 579 GLU cc_start: 0.8694 (mp0) cc_final: 0.8057 (mp0) REVERT: D 614 ASP cc_start: 0.8537 (p0) cc_final: 0.8197 (p0) REVERT: A 334 LEU cc_start: 0.9225 (OUTLIER) cc_final: 0.8807 (mt) REVERT: A 344 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.7586 (ttp-170) REVERT: A 399 MET cc_start: 0.8503 (mtt) cc_final: 0.8231 (mtt) REVERT: A 522 ASP cc_start: 0.8348 (t0) cc_final: 0.7930 (t0) REVERT: A 579 GLU cc_start: 0.8091 (tm-30) cc_final: 0.7412 (tm-30) REVERT: A 611 ASP cc_start: 0.8886 (t70) cc_final: 0.8667 (p0) REVERT: A 660 GLN cc_start: 0.8582 (mp10) cc_final: 0.8075 (mp10) REVERT: A 681 ILE cc_start: 0.8407 (OUTLIER) cc_final: 0.8110 (mm) REVERT: A 684 MET cc_start: 0.9144 (OUTLIER) cc_final: 0.8536 (ttp) outliers start: 68 outliers final: 59 residues processed: 262 average time/residue: 0.3114 time to fit residues: 123.8367 Evaluate side-chains 275 residues out of total 2049 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 210 time to evaluate : 2.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 334 LEU Chi-restraints excluded: chain C residue 371 ILE Chi-restraints excluded: chain C residue 377 LYS Chi-restraints excluded: chain C residue 435 LYS Chi-restraints excluded: chain C residue 448 ASP Chi-restraints excluded: chain C residue 455 SER Chi-restraints excluded: chain C residue 529 GLN Chi-restraints excluded: chain C residue 544 ILE Chi-restraints excluded: chain C residue 599 THR Chi-restraints excluded: chain C residue 624 VAL Chi-restraints excluded: chain C residue 659 ILE Chi-restraints excluded: chain C residue 681 ILE Chi-restraints excluded: chain C residue 695 ASP Chi-restraints excluded: chain B residue 342 THR Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 447 ASP Chi-restraints excluded: chain B residue 522 ASP Chi-restraints excluded: chain B residue 525 VAL Chi-restraints excluded: chain B residue 534 ASP Chi-restraints excluded: chain B residue 611 ASP Chi-restraints excluded: chain B residue 624 VAL Chi-restraints excluded: chain F residue 363 LEU Chi-restraints excluded: chain F residue 442 THR Chi-restraints excluded: chain F residue 448 ASP Chi-restraints excluded: chain F residue 461 LEU Chi-restraints excluded: chain F residue 593 ASN Chi-restraints excluded: chain F residue 629 HIS Chi-restraints excluded: chain E residue 346 ASP Chi-restraints excluded: chain E residue 354 SER Chi-restraints excluded: chain E residue 363 LEU Chi-restraints excluded: chain E residue 371 ILE Chi-restraints excluded: chain E residue 498 LEU Chi-restraints excluded: chain E residue 531 ILE Chi-restraints excluded: chain E residue 574 ILE Chi-restraints excluded: chain E residue 599 THR Chi-restraints excluded: chain E residue 681 ILE Chi-restraints excluded: chain D residue 351 ILE Chi-restraints excluded: chain D residue 365 THR Chi-restraints excluded: chain D residue 370 SER Chi-restraints excluded: chain D residue 372 ARG Chi-restraints excluded: chain D residue 399 MET Chi-restraints excluded: chain D residue 440 VAL Chi-restraints excluded: chain D residue 455 SER Chi-restraints excluded: chain D residue 554 PHE Chi-restraints excluded: chain D residue 558 LEU Chi-restraints excluded: chain D residue 611 ASP Chi-restraints excluded: chain D residue 621 ILE Chi-restraints excluded: chain D residue 680 HIS Chi-restraints excluded: chain D residue 695 ASP Chi-restraints excluded: chain D residue 699 TYR Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 344 ARG Chi-restraints excluded: chain A residue 432 ASP Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 507 THR Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 581 CYS Chi-restraints excluded: chain A residue 592 ILE Chi-restraints excluded: chain A residue 593 ASN Chi-restraints excluded: chain A residue 615 ASN Chi-restraints excluded: chain A residue 643 ASP Chi-restraints excluded: chain A residue 681 ILE Chi-restraints excluded: chain A residue 684 MET Chi-restraints excluded: chain A residue 695 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 221 random chunks: chunk 186 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 161 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 chunk 175 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 154 optimal weight: 0.8980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 529 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.123304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.090142 restraints weight = 28771.398| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.53 r_work: 0.2857 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 18837 Z= 0.259 Angle : 0.601 8.500 25495 Z= 0.288 Chirality : 0.042 0.288 2836 Planarity : 0.003 0.035 3229 Dihedral : 9.068 160.348 2564 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.39 % Favored : 93.57 % Rotamer: Outliers : 3.37 % Allowed : 25.77 % Favored : 70.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.18), residues: 2239 helix: 1.24 (0.20), residues: 701 sheet: -0.94 (0.31), residues: 310 loop : -1.09 (0.18), residues: 1228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 675 HIS 0.004 0.001 HIS D 680 PHE 0.012 0.001 PHE C 502 TYR 0.018 0.001 TYR B 482 ARG 0.005 0.000 ARG C 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3730.58 seconds wall clock time: 69 minutes 3.68 seconds (4143.68 seconds total)