Starting phenix.real_space_refine on Wed Feb 14 08:31:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/02_2024/8k3u_36861_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/02_2024/8k3u_36861.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/02_2024/8k3u_36861.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/02_2024/8k3u_36861.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/02_2024/8k3u_36861_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3u_36861/02_2024/8k3u_36861_updated.pdb" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.091 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 6 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 5792 2.51 5 N 1440 2.21 5 O 1614 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 500": "OD1" <-> "OD2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1030": "OE1" <-> "OE2" Residue "A TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1060": "OE1" <-> "OE2" Residue "A ASP 1066": "OD1" <-> "OD2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 475": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B ASP 661": "OD1" <-> "OD2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 741": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 776": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 795": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 831": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 842": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1030": "OE1" <-> "OE2" Residue "B TYR 1035": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1060": "OE1" <-> "OE2" Residue "B ASP 1066": "OD1" <-> "OD2" Residue "B TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8914 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4374 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 16, 'TRANS': 580} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 656 Unresolved non-hydrogen dihedrals: 437 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 7, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 283 Chain: "B" Number of atoms: 4360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4360 Classifications: {'peptide': 597} Incomplete info: {'truncation_to_alanine': 133} Link IDs: {'PTRANS': 16, 'TRANS': 580} Chain breaks: 7 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 534 Unresolved non-hydrogen angles: 677 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 46 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 3, 'TYR:plan': 5, 'ASN:plan1': 6, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 8, 'GLU:plan': 13, 'ARG:plan': 12} Unresolved non-hydrogen planarities: 294 Chain: "A" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 90 Unusual residues: {' MG': 2, 'NAG': 1, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 90 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 90 Unusual residues: {' MG': 2, 'NAG': 1, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.51, per 1000 atoms: 0.62 Number of scatterers: 8914 At special positions: 0 Unit cell: (132.5, 75.26, 96.46, 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 58 16.00 P 6 15.00 Mg 4 11.99 O 1614 8.00 N 1440 7.00 C 5792 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.8 seconds 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 6 sheets defined 56.3% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 425 through 427 No H-bonds generated for 'chain 'A' and resid 425 through 427' Processing helix chain 'A' and resid 459 through 478 removed outlier: 3.612A pdb=" N THR A 465 " --> pdb=" O LEU A 461 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 471 " --> pdb=" O LYS A 467 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASN A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 507 through 515 Processing helix chain 'A' and resid 578 through 586 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 611 through 618 removed outlier: 3.846A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 639 No H-bonds generated for 'chain 'A' and resid 637 through 639' Processing helix chain 'A' and resid 651 through 668 removed outlier: 3.502A pdb=" N MET A 656 " --> pdb=" O PHE A 652 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER A 657 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 686 No H-bonds generated for 'chain 'A' and resid 683 through 686' Processing helix chain 'A' and resid 689 through 695 Processing helix chain 'A' and resid 719 through 725 Processing helix chain 'A' and resid 750 through 773 removed outlier: 4.157A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 780 Processing helix chain 'A' and resid 785 through 806 Processing helix chain 'A' and resid 808 through 824 Processing helix chain 'A' and resid 829 through 854 removed outlier: 4.570A pdb=" N VAL A 833 " --> pdb=" O SER A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 889 Processing helix chain 'A' and resid 915 through 931 Processing helix chain 'A' and resid 936 through 939 Processing helix chain 'A' and resid 942 through 953 removed outlier: 4.157A pdb=" N LEU A 947 " --> pdb=" O GLN A 944 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU A 948 " --> pdb=" O TYR A 945 " (cutoff:3.500A) Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 1029 through 1056 removed outlier: 3.625A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1074 Processing helix chain 'A' and resid 1092 through 1126 removed outlier: 3.519A pdb=" N ILE A1101 " --> pdb=" O TYR A1097 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 459 through 478 removed outlier: 3.611A pdb=" N THR B 465 " --> pdb=" O LEU B 461 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 471 " --> pdb=" O LYS B 467 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ASN B 472 " --> pdb=" O GLY B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 507 through 515 Processing helix chain 'B' and resid 578 through 586 Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 618 removed outlier: 3.845A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 639 No H-bonds generated for 'chain 'B' and resid 637 through 639' Processing helix chain 'B' and resid 651 through 668 removed outlier: 3.502A pdb=" N MET B 656 " --> pdb=" O PHE B 652 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER B 657 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N PHE B 668 " --> pdb=" O THR B 664 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 686 No H-bonds generated for 'chain 'B' and resid 683 through 686' Processing helix chain 'B' and resid 689 through 695 Processing helix chain 'B' and resid 719 through 725 Processing helix chain 'B' and resid 750 through 773 removed outlier: 4.158A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 775 through 780 Processing helix chain 'B' and resid 785 through 806 Processing helix chain 'B' and resid 808 through 824 Processing helix chain 'B' and resid 829 through 854 removed outlier: 4.570A pdb=" N VAL B 833 " --> pdb=" O SER B 829 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 889 Processing helix chain 'B' and resid 915 through 931 Processing helix chain 'B' and resid 936 through 939 Processing helix chain 'B' and resid 942 through 953 removed outlier: 4.157A pdb=" N LEU B 947 " --> pdb=" O GLN B 944 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU B 948 " --> pdb=" O TYR B 945 " (cutoff:3.500A) Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 1029 through 1056 removed outlier: 3.626A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1074 Processing helix chain 'B' and resid 1092 through 1126 removed outlier: 3.519A pdb=" N ILE B1101 " --> pdb=" O TYR B1097 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 417 through 421 removed outlier: 3.752A pdb=" N ARG A 417 " --> pdb=" O GLU A 539 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLU A 539 " --> pdb=" O ARG A 417 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE A 493 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N LEU A 568 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL A 495 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 605 through 607 removed outlier: 4.133A pdb=" N GLU A 630 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N SER A 739 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 11.484A pdb=" N ARG A 632 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 9.559A pdb=" N TYR A 741 " --> pdb=" O ARG A 632 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.851A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.753A pdb=" N ARG B 417 " --> pdb=" O GLU B 539 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU B 539 " --> pdb=" O ARG B 417 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N ILE B 493 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N LEU B 568 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N VAL B 495 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 605 through 607 removed outlier: 4.133A pdb=" N GLU B 630 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 8.552A pdb=" N SER B 739 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 11.484A pdb=" N ARG B 632 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 9.561A pdb=" N TYR B 741 " --> pdb=" O ARG B 632 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.851A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) 502 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.74 Time building geometry restraints manager: 4.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1364 1.31 - 1.43: 2622 1.43 - 1.56: 5004 1.56 - 1.69: 28 1.69 - 1.81: 86 Bond restraints: 9104 Sorted by residual: bond pdb=" C31 POV B1201 " pdb=" O31 POV B1201 " ideal model delta sigma weight residual 1.327 1.433 -0.106 2.00e-02 2.50e+03 2.80e+01 bond pdb=" C31 POV A1505 " pdb=" O31 POV A1505 " ideal model delta sigma weight residual 1.327 1.432 -0.105 2.00e-02 2.50e+03 2.74e+01 bond pdb="C312 POV B1201 " pdb="C313 POV B1201 " ideal model delta sigma weight residual 1.523 1.604 -0.081 2.00e-02 2.50e+03 1.64e+01 bond pdb="C312 POV A1505 " pdb="C313 POV A1505 " ideal model delta sigma weight residual 1.523 1.603 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C21 POV B1201 " pdb=" O21 POV B1201 " ideal model delta sigma weight residual 1.330 1.405 -0.075 2.00e-02 2.50e+03 1.42e+01 ... (remaining 9099 not shown) Histogram of bond angle deviations from ideal: 98.84 - 105.89: 145 105.89 - 112.93: 4989 112.93 - 119.97: 3224 119.97 - 127.01: 3960 127.01 - 134.06: 73 Bond angle restraints: 12391 Sorted by residual: angle pdb=" N LEU B 939 " pdb=" CA LEU B 939 " pdb=" C LEU B 939 " ideal model delta sigma weight residual 114.39 106.13 8.26 1.45e+00 4.76e-01 3.25e+01 angle pdb=" N ARG A 718 " pdb=" CA ARG A 718 " pdb=" C ARG A 718 " ideal model delta sigma weight residual 114.12 106.26 7.86 1.39e+00 5.18e-01 3.20e+01 angle pdb=" N ARG B 718 " pdb=" CA ARG B 718 " pdb=" C ARG B 718 " ideal model delta sigma weight residual 114.12 106.27 7.85 1.39e+00 5.18e-01 3.19e+01 angle pdb=" N LEU A 939 " pdb=" CA LEU A 939 " pdb=" C LEU A 939 " ideal model delta sigma weight residual 114.39 106.21 8.18 1.45e+00 4.76e-01 3.18e+01 angle pdb=" N LEU B 642 " pdb=" CA LEU B 642 " pdb=" C LEU B 642 " ideal model delta sigma weight residual 112.87 107.18 5.69 1.20e+00 6.94e-01 2.25e+01 ... (remaining 12386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.41: 4984 21.41 - 42.81: 260 42.81 - 64.22: 84 64.22 - 85.62: 22 85.62 - 107.03: 6 Dihedral angle restraints: 5356 sinusoidal: 1842 harmonic: 3514 Sorted by residual: dihedral pdb=" CA VAL B 673 " pdb=" C VAL B 673 " pdb=" N LEU B 674 " pdb=" CA LEU B 674 " ideal model delta harmonic sigma weight residual 180.00 155.77 24.23 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA VAL A 673 " pdb=" C VAL A 673 " pdb=" N LEU A 674 " pdb=" CA LEU A 674 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 dihedral pdb=" C27 POV A1505 " pdb=" C28 POV A1505 " pdb=" C29 POV A1505 " pdb="C210 POV A1505 " ideal model delta sinusoidal sigma weight residual 127.48 -125.49 -107.03 1 3.00e+01 1.11e-03 1.38e+01 ... (remaining 5353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 883 0.045 - 0.089: 331 0.089 - 0.134: 158 0.134 - 0.178: 71 0.178 - 0.223: 12 Chirality restraints: 1455 Sorted by residual: chirality pdb=" CA ILE A1096 " pdb=" N ILE A1096 " pdb=" C ILE A1096 " pdb=" CB ILE A1096 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ILE B1096 " pdb=" N ILE B1096 " pdb=" C ILE B1096 " pdb=" CB ILE B1096 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA LEU B 939 " pdb=" N LEU B 939 " pdb=" C LEU B 939 " pdb=" CB LEU B 939 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 ... (remaining 1452 not shown) Planarity restraints: 1516 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 674 " 0.048 5.00e-02 4.00e+02 7.25e-02 8.42e+00 pdb=" N PRO B 675 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO B 675 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO B 675 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 674 " 0.048 5.00e-02 4.00e+02 7.24e-02 8.39e+00 pdb=" N PRO A 675 " -0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 675 " 0.038 5.00e-02 4.00e+02 pdb=" CD PRO A 675 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 750 " -0.029 5.00e-02 4.00e+02 4.38e-02 3.08e+00 pdb=" N PRO B 751 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO B 751 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 751 " -0.025 5.00e-02 4.00e+02 ... (remaining 1513 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 148 2.64 - 3.20: 8767 3.20 - 3.77: 13938 3.77 - 4.33: 18904 4.33 - 4.90: 31002 Nonbonded interactions: 72759 Sorted by model distance: nonbonded pdb="MG MG A1501 " pdb=" O1A UDP A1504 " model vdw 2.072 2.170 nonbonded pdb="MG MG B1202 " pdb=" O1A UDP B1205 " model vdw 2.073 2.170 nonbonded pdb="MG MG B1203 " pdb=" O3' UDP B1205 " model vdw 2.163 2.170 nonbonded pdb="MG MG A1502 " pdb=" O3' UDP A1504 " model vdw 2.163 2.170 nonbonded pdb=" O CYS A 845 " pdb=" OG1 THR A 849 " model vdw 2.230 2.440 ... (remaining 72754 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 415 through 936 or (resid 937 and (name N or name CA or na \ me C or name O or name CB )) or resid 938 through 941 or (resid 942 through 945 \ and (name N or name CA or name C or name O or name CB )) or resid 946 or (resid \ 947 and (name N or name CA or name C or name O or name CB )) or resid 948 throug \ h 1127 or resid 1502)) selection = (chain 'B' and (resid 415 through 1127 or resid 1202)) } 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: 0.650 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: 2.790 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.230 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6504 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.106 9104 Z= 0.565 Angle : 1.065 12.052 12391 Z= 0.696 Chirality : 0.064 0.223 1455 Planarity : 0.005 0.073 1516 Dihedral : 16.046 107.027 3076 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.85 % Favored : 93.98 % Rotamer: Outliers : 0.73 % Allowed : 2.56 % Favored : 96.71 % 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: -1.45 (0.23), residues: 1162 helix: -0.39 (0.18), residues: 686 sheet: -1.15 (0.43), residues: 142 loop : -1.77 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 616 HIS 0.002 0.001 HIS B 783 PHE 0.021 0.002 PHE A 812 TYR 0.027 0.002 TYR A 865 ARG 0.008 0.001 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 580 ASN cc_start: 0.7250 (m110) cc_final: 0.7050 (m110) REVERT: B 580 ASN cc_start: 0.7412 (m110) cc_final: 0.7148 (m110) REVERT: B 661 ASP cc_start: 0.7689 (m-30) cc_final: 0.7423 (m-30) REVERT: B 665 GLU cc_start: 0.7518 (mt-10) cc_final: 0.7016 (mt-10) REVERT: B 772 PHE cc_start: 0.6997 (t80) cc_final: 0.6545 (t80) outliers start: 6 outliers final: 2 residues processed: 180 average time/residue: 0.2084 time to fit residues: 51.8201 Evaluate side-chains 135 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 133 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain B residue 946 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.6980 chunk 89 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 47 optimal weight: 8.9990 chunk 92 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 ASN ** B 614 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6619 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9104 Z= 0.253 Angle : 0.566 5.611 12391 Z= 0.309 Chirality : 0.042 0.196 1455 Planarity : 0.004 0.057 1516 Dihedral : 13.634 93.644 1456 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.93 % Favored : 96.90 % Rotamer: Outliers : 1.46 % Allowed : 11.81 % Favored : 86.72 % 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: -0.32 (0.24), residues: 1162 helix: 0.56 (0.19), residues: 684 sheet: -0.95 (0.42), residues: 136 loop : -1.28 (0.30), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 490 HIS 0.002 0.001 HIS A 582 PHE 0.019 0.002 PHE A 678 TYR 0.017 0.002 TYR B 925 ARG 0.005 0.001 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 148 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 443 PRO cc_start: 0.8130 (Cg_exo) cc_final: 0.7891 (Cg_endo) REVERT: A 580 ASN cc_start: 0.7529 (m110) cc_final: 0.7292 (m110) REVERT: A 772 PHE cc_start: 0.7142 (t80) cc_final: 0.6845 (t80) REVERT: A 1070 MET cc_start: 0.6225 (mtt) cc_final: 0.5727 (mtt) REVERT: A 1121 ILE cc_start: 0.8144 (mm) cc_final: 0.7903 (mm) REVERT: B 449 MET cc_start: 0.7585 (ttm) cc_final: 0.7251 (ttp) REVERT: B 580 ASN cc_start: 0.7429 (m110) cc_final: 0.7198 (m110) REVERT: B 665 GLU cc_start: 0.7373 (mt-10) cc_final: 0.7014 (mt-10) REVERT: B 1070 MET cc_start: 0.6401 (mtt) cc_final: 0.5968 (mtt) outliers start: 12 outliers final: 7 residues processed: 160 average time/residue: 0.1773 time to fit residues: 41.2713 Evaluate side-chains 129 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 122 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 948 LEU Chi-restraints excluded: chain B residue 1117 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 20.0000 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 8.9990 chunk 72 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 107 optimal weight: 0.5980 chunk 115 optimal weight: 0.9990 chunk 95 optimal weight: 0.7980 chunk 106 optimal weight: 8.9990 chunk 36 optimal weight: 0.9980 chunk 86 optimal weight: 7.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A 575 ASN A 957 ASN B 472 ASN B 614 GLN B 957 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.2786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9104 Z= 0.172 Angle : 0.477 6.116 12391 Z= 0.258 Chirality : 0.040 0.167 1455 Planarity : 0.003 0.036 1516 Dihedral : 13.342 87.903 1454 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.73 % Rotamer: Outliers : 1.10 % Allowed : 14.86 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.24), residues: 1162 helix: 1.35 (0.20), residues: 668 sheet: -0.79 (0.43), residues: 146 loop : -0.94 (0.31), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 490 HIS 0.003 0.001 HIS B 783 PHE 0.013 0.001 PHE B 619 TYR 0.015 0.001 TYR A 842 ARG 0.003 0.000 ARG A 718 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 142 time to evaluate : 0.985 Fit side-chains revert: symmetry clash REVERT: A 580 ASN cc_start: 0.7356 (m110) cc_final: 0.7061 (m110) REVERT: A 748 GLU cc_start: 0.4499 (pm20) cc_final: 0.4112 (mt-10) REVERT: A 772 PHE cc_start: 0.7032 (t80) cc_final: 0.6716 (t80) REVERT: A 938 MET cc_start: 0.6522 (ttm) cc_final: 0.6050 (tpp) REVERT: B 535 MET cc_start: 0.6004 (ttt) cc_final: 0.5557 (mmm) REVERT: B 580 ASN cc_start: 0.7323 (m110) cc_final: 0.7103 (m110) REVERT: B 748 GLU cc_start: 0.4495 (pm20) cc_final: 0.4064 (mt-10) REVERT: B 772 PHE cc_start: 0.7023 (t80) cc_final: 0.6670 (t80) REVERT: B 938 MET cc_start: 0.6544 (ttm) cc_final: 0.6209 (tpp) outliers start: 9 outliers final: 5 residues processed: 150 average time/residue: 0.1675 time to fit residues: 37.2077 Evaluate side-chains 133 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 128 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 948 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 9.9990 chunk 80 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 chunk 51 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 114 optimal weight: 0.5980 chunk 56 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9104 Z= 0.251 Angle : 0.532 5.451 12391 Z= 0.289 Chirality : 0.042 0.243 1455 Planarity : 0.003 0.031 1516 Dihedral : 13.108 91.699 1452 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.36 % Favored : 96.47 % Rotamer: Outliers : 4.14 % Allowed : 14.49 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1162 helix: 1.24 (0.20), residues: 662 sheet: -0.63 (0.42), residues: 152 loop : -0.83 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 806 HIS 0.002 0.001 HIS A 536 PHE 0.021 0.002 PHE B1052 TYR 0.015 0.001 TYR B 681 ARG 0.004 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 131 time to evaluate : 1.006 Fit side-chains revert: symmetry clash REVERT: A 568 LEU cc_start: 0.7555 (OUTLIER) cc_final: 0.7227 (mp) REVERT: A 580 ASN cc_start: 0.7366 (m110) cc_final: 0.7072 (m110) REVERT: A 772 PHE cc_start: 0.7134 (t80) cc_final: 0.6867 (t80) REVERT: A 938 MET cc_start: 0.6319 (ttm) cc_final: 0.6083 (tpp) REVERT: A 1070 MET cc_start: 0.6526 (mtt) cc_final: 0.6211 (mtt) REVERT: B 535 MET cc_start: 0.5975 (ttt) cc_final: 0.5731 (mmm) REVERT: B 568 LEU cc_start: 0.7445 (OUTLIER) cc_final: 0.7091 (mp) REVERT: B 580 ASN cc_start: 0.7356 (m110) cc_final: 0.7132 (m110) REVERT: B 748 GLU cc_start: 0.4180 (pm20) cc_final: 0.3930 (mt-10) REVERT: B 938 MET cc_start: 0.6572 (ttm) cc_final: 0.6325 (tpp) REVERT: B 1070 MET cc_start: 0.6478 (mtt) cc_final: 0.6106 (mtt) REVERT: B 1120 MET cc_start: 0.8088 (mmt) cc_final: 0.7752 (mmm) outliers start: 34 outliers final: 19 residues processed: 159 average time/residue: 0.2006 time to fit residues: 48.1114 Evaluate side-chains 144 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 123 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 861 THR Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 861 THR Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1050 THR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 1.9990 chunk 64 optimal weight: 0.5980 chunk 1 optimal weight: 0.0170 chunk 84 optimal weight: 4.9990 chunk 47 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 58 optimal weight: 7.9990 chunk 102 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 overall best weight: 1.1822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6647 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9104 Z= 0.208 Angle : 0.504 5.745 12391 Z= 0.272 Chirality : 0.040 0.190 1455 Planarity : 0.003 0.029 1516 Dihedral : 12.392 89.420 1452 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.67 % Favored : 97.16 % Rotamer: Outliers : 3.90 % Allowed : 16.32 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1162 helix: 1.31 (0.20), residues: 664 sheet: -0.62 (0.41), residues: 152 loop : -0.73 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 806 HIS 0.002 0.001 HIS A 536 PHE 0.016 0.002 PHE A 813 TYR 0.015 0.001 TYR B 455 ARG 0.003 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 130 time to evaluate : 1.051 Fit side-chains REVERT: A 568 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7192 (mp) REVERT: A 580 ASN cc_start: 0.7295 (m110) cc_final: 0.6996 (m110) REVERT: A 772 PHE cc_start: 0.7052 (t80) cc_final: 0.6766 (t80) REVERT: A 794 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7035 (tm-30) REVERT: A 1070 MET cc_start: 0.6598 (mtt) cc_final: 0.6216 (mtt) REVERT: B 535 MET cc_start: 0.6161 (ttt) cc_final: 0.5850 (mmm) REVERT: B 568 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7126 (mp) REVERT: B 580 ASN cc_start: 0.7296 (m110) cc_final: 0.7066 (m110) REVERT: B 748 GLU cc_start: 0.4274 (pm20) cc_final: 0.3722 (tp30) REVERT: B 794 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6943 (tm-30) REVERT: B 1070 MET cc_start: 0.6583 (mtt) cc_final: 0.6215 (mtt) REVERT: B 1120 MET cc_start: 0.7931 (mmt) cc_final: 0.7593 (mmm) outliers start: 32 outliers final: 17 residues processed: 156 average time/residue: 0.1696 time to fit residues: 39.3074 Evaluate side-chains 137 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1050 THR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 4.9990 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 59 optimal weight: 20.0000 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6681 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9104 Z= 0.239 Angle : 0.539 6.405 12391 Z= 0.289 Chirality : 0.041 0.171 1455 Planarity : 0.003 0.026 1516 Dihedral : 12.122 88.181 1452 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.18 % Favored : 96.64 % Rotamer: Outliers : 3.53 % Allowed : 17.54 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1162 helix: 1.21 (0.20), residues: 664 sheet: -0.64 (0.41), residues: 152 loop : -0.77 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 806 HIS 0.002 0.001 HIS A 536 PHE 0.032 0.002 PHE A 942 TYR 0.018 0.001 TYR A 455 ARG 0.002 0.000 ARG A 682 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 128 time to evaluate : 0.994 Fit side-chains REVERT: A 568 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7215 (mp) REVERT: A 580 ASN cc_start: 0.7298 (m110) cc_final: 0.6976 (m110) REVERT: A 794 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6392 (tm-30) REVERT: A 1070 MET cc_start: 0.6632 (mtt) cc_final: 0.6329 (mtt) REVERT: B 568 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7183 (mp) REVERT: B 580 ASN cc_start: 0.7334 (m110) cc_final: 0.7093 (m110) REVERT: B 748 GLU cc_start: 0.4299 (pm20) cc_final: 0.3734 (tp30) REVERT: B 1120 MET cc_start: 0.7875 (mmt) cc_final: 0.7581 (mmm) outliers start: 29 outliers final: 21 residues processed: 146 average time/residue: 0.1663 time to fit residues: 36.2934 Evaluate side-chains 142 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 0.867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 1045 ILE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1050 THR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 0.9990 chunk 12 optimal weight: 9.9990 chunk 65 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 69 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9104 Z= 0.220 Angle : 0.524 7.048 12391 Z= 0.281 Chirality : 0.040 0.151 1455 Planarity : 0.003 0.023 1516 Dihedral : 10.875 81.620 1452 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.17 % Allowed : 2.84 % Favored : 96.99 % Rotamer: Outliers : 3.65 % Allowed : 18.39 % Favored : 77.95 % 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 (0.25), residues: 1162 helix: 1.19 (0.20), residues: 672 sheet: -0.60 (0.41), residues: 152 loop : -0.67 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.002 0.001 HIS A 937 PHE 0.041 0.002 PHE A 942 TYR 0.019 0.001 TYR B 842 ARG 0.002 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 122 time to evaluate : 1.019 Fit side-chains REVERT: A 568 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7292 (mp) REVERT: A 794 GLU cc_start: 0.7338 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: A 1070 MET cc_start: 0.6712 (mtt) cc_final: 0.6435 (mtt) REVERT: B 568 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7278 (mp) REVERT: B 580 ASN cc_start: 0.7296 (m110) cc_final: 0.7061 (m110) REVERT: B 748 GLU cc_start: 0.4461 (pm20) cc_final: 0.3580 (tp30) REVERT: B 1120 MET cc_start: 0.7746 (mmt) cc_final: 0.7488 (mmm) outliers start: 30 outliers final: 24 residues processed: 144 average time/residue: 0.1640 time to fit residues: 35.6585 Evaluate side-chains 141 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1050 THR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 67 optimal weight: 0.3980 chunk 34 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 77 optimal weight: 0.0470 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.6884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 957 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6707 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9104 Z= 0.264 Angle : 0.554 7.308 12391 Z= 0.296 Chirality : 0.041 0.150 1455 Planarity : 0.003 0.026 1516 Dihedral : 10.097 85.049 1452 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.36 % Favored : 96.47 % Rotamer: Outliers : 3.90 % Allowed : 19.00 % Favored : 77.10 % 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: 0.27 (0.24), residues: 1162 helix: 0.89 (0.20), residues: 682 sheet: -0.62 (0.40), residues: 152 loop : -0.73 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 806 HIS 0.002 0.001 HIS A 536 PHE 0.034 0.002 PHE A 942 TYR 0.018 0.001 TYR B 842 ARG 0.002 0.000 ARG B 682 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 115 time to evaluate : 0.918 Fit side-chains REVERT: A 568 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7387 (mp) REVERT: A 794 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.6472 (tm-30) REVERT: B 568 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7274 (mp) REVERT: B 748 GLU cc_start: 0.4301 (pm20) cc_final: 0.3711 (tp30) REVERT: B 1120 MET cc_start: 0.7557 (mmt) cc_final: 0.7320 (mmm) outliers start: 32 outliers final: 26 residues processed: 138 average time/residue: 0.1600 time to fit residues: 33.1894 Evaluate side-chains 141 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 802 THR Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 541 THR Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 802 THR Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1050 THR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 69 optimal weight: 0.2980 chunk 112 optimal weight: 0.6980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9104 Z= 0.181 Angle : 0.499 7.775 12391 Z= 0.263 Chirality : 0.039 0.135 1455 Planarity : 0.002 0.021 1516 Dihedral : 9.549 74.894 1452 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.50 % Favored : 97.42 % Rotamer: Outliers : 3.05 % Allowed : 20.22 % Favored : 76.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1162 helix: 1.23 (0.20), residues: 672 sheet: -0.47 (0.41), residues: 152 loop : -0.57 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.002 0.001 HIS A 783 PHE 0.016 0.001 PHE B 813 TYR 0.019 0.001 TYR B 842 ARG 0.002 0.000 ARG B 759 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 0.977 Fit side-chains REVERT: A 535 MET cc_start: 0.6068 (OUTLIER) cc_final: 0.5435 (mmm) REVERT: A 568 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7416 (mp) REVERT: A 794 GLU cc_start: 0.7214 (OUTLIER) cc_final: 0.6366 (tm-30) REVERT: A 938 MET cc_start: 0.7124 (tpp) cc_final: 0.6848 (tpp) REVERT: A 1117 SER cc_start: 0.8648 (OUTLIER) cc_final: 0.8437 (p) REVERT: B 580 ASN cc_start: 0.7232 (m110) cc_final: 0.7011 (m110) REVERT: B 748 GLU cc_start: 0.4413 (pm20) cc_final: 0.3558 (tp30) outliers start: 25 outliers final: 20 residues processed: 142 average time/residue: 0.1583 time to fit residues: 33.9132 Evaluate side-chains 141 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 117 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 518 CYS Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 775 PHE Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 942 PHE Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1050 THR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 117 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 93 optimal weight: 0.0070 chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 57 optimal weight: 0.7980 chunk 74 optimal weight: 0.7980 chunk 99 optimal weight: 0.3980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.4331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9104 Z= 0.144 Angle : 0.476 8.320 12391 Z= 0.251 Chirality : 0.039 0.130 1455 Planarity : 0.002 0.023 1516 Dihedral : 9.207 71.723 1452 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.84 % Favored : 97.07 % Rotamer: Outliers : 3.05 % Allowed : 20.34 % Favored : 76.61 % 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: 0.91 (0.25), residues: 1162 helix: 1.44 (0.20), residues: 672 sheet: -0.31 (0.42), residues: 152 loop : -0.52 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A1047 HIS 0.003 0.001 HIS A 783 PHE 0.016 0.001 PHE A 619 TYR 0.012 0.001 TYR B 681 ARG 0.002 0.000 ARG A1040 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2324 Ramachandran restraints generated. 1162 Oldfield, 0 Emsley, 1162 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.000 Fit side-chains REVERT: A 535 MET cc_start: 0.5991 (OUTLIER) cc_final: 0.5405 (mmm) REVERT: A 807 PHE cc_start: 0.7651 (m-80) cc_final: 0.7397 (m-80) REVERT: A 1117 SER cc_start: 0.8633 (OUTLIER) cc_final: 0.8413 (p) REVERT: B 580 ASN cc_start: 0.7093 (m110) cc_final: 0.6829 (m110) REVERT: B 723 GLU cc_start: 0.6508 (tp30) cc_final: 0.6235 (mm-30) REVERT: B 748 GLU cc_start: 0.4382 (pm20) cc_final: 0.3459 (tp30) outliers start: 25 outliers final: 19 residues processed: 143 average time/residue: 0.1558 time to fit residues: 33.9738 Evaluate side-chains 143 residues out of total 1084 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 122 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 426 ASN Chi-restraints excluded: chain A residue 476 MET Chi-restraints excluded: chain A residue 535 MET Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 640 VAL Chi-restraints excluded: chain A residue 835 SER Chi-restraints excluded: chain A residue 865 TYR Chi-restraints excluded: chain A residue 1050 THR Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1117 SER Chi-restraints excluded: chain B residue 476 MET Chi-restraints excluded: chain B residue 518 CYS Chi-restraints excluded: chain B residue 542 THR Chi-restraints excluded: chain B residue 568 LEU Chi-restraints excluded: chain B residue 640 VAL Chi-restraints excluded: chain B residue 775 PHE Chi-restraints excluded: chain B residue 835 SER Chi-restraints excluded: chain B residue 865 TYR Chi-restraints excluded: chain B residue 1050 THR Chi-restraints excluded: chain B residue 1066 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 17 optimal weight: 5.9990 chunk 82 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.217491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.176836 restraints weight = 9926.870| |-----------------------------------------------------------------------------| r_work (start): 0.4112 rms_B_bonded: 3.42 r_work: 0.3887 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.4250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 9104 Z= 0.256 Angle : 0.572 15.390 12391 Z= 0.295 Chirality : 0.041 0.139 1455 Planarity : 0.003 0.022 1516 Dihedral : 9.591 72.121 1452 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 10.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.01 % Favored : 96.90 % Rotamer: Outliers : 2.80 % Allowed : 19.85 % Favored : 77.34 % 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 (0.24), residues: 1162 helix: 1.16 (0.20), residues: 672 sheet: -0.38 (0.42), residues: 152 loop : -0.63 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B1047 HIS 0.002 0.001 HIS A 783 PHE 0.019 0.002 PHE B 813 TYR 0.019 0.001 TYR B 455 ARG 0.002 0.000 ARG B 682 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.20 seconds wall clock time: 34 minutes 30.91 seconds (2070.91 seconds total)