Starting phenix.real_space_refine on Sun Apr 7 17:18:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/04_2024/8k3r_36857_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/04_2024/8k3r_36857.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/04_2024/8k3r_36857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/04_2024/8k3r_36857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/04_2024/8k3r_36857_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/04_2024/8k3r_36857_updated.pdb" } resolution = 3.51 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= 0.006 sd= 0.060 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 66 5.16 5 C 7258 2.51 5 N 1781 2.21 5 O 1954 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 458": "OD1" <-> "OD2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 553": "OE1" <-> "OE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 618": "OE1" <-> "OE2" Residue "A PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 634": "OD1" <-> "OD2" Residue "A GLU 653": "OE1" <-> "OE2" Residue "A ASP 661": "OD1" <-> "OD2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 684": "OE1" <-> "OE2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 703": "OE1" <-> "OE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A GLU 723": "OE1" <-> "OE2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 913": "OD1" <-> "OD2" Residue "A TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 1006": "OD1" <-> "OD2" Residue "A TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 378": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 458": "OD1" <-> "OD2" Residue "B ASP 471": "OD1" <-> "OD2" Residue "B TYR 519": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 553": "OE1" <-> "OE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 618": "OE1" <-> "OE2" Residue "B PHE 619": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 634": "OD1" <-> "OD2" Residue "B GLU 653": "OE1" <-> "OE2" Residue "B ASP 661": "OD1" <-> "OD2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 684": "OE1" <-> "OE2" Residue "B TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 703": "OE1" <-> "OE2" Residue "B ASP 717": "OD1" <-> "OD2" Residue "B GLU 723": "OE1" <-> "OE2" Residue "B TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 794": "OE1" <-> "OE2" Residue "B PHE 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 827": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 862": "OE1" <-> "OE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 885": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 913": "OD1" <-> "OD2" Residue "B TYR 932": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1005": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1006": "OD1" <-> "OD2" Residue "B TYR 1036": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1067": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 11061 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5482 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 20, 'TRANS': 681} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 251 Unresolved non-hydrogen angles: 313 Unresolved non-hydrogen dihedrals: 211 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 5483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 702, 5483 Classifications: {'peptide': 702} Incomplete info: {'truncation_to_alanine': 66} Link IDs: {'PTRANS': 20, 'TRANS': 681} Chain breaks: 5 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 250 Unresolved non-hydrogen angles: 311 Unresolved non-hydrogen dihedrals: 210 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 4, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 139 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 6.19, per 1000 atoms: 0.56 Number of scatterers: 11061 At special positions: 0 Unit cell: (119.78, 98.58, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 66 16.00 P 2 15.00 O 1954 8.00 N 1781 7.00 C 7258 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: 4.13 Conformation dependent library (CDL) restraints added in 2.0 seconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2678 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 6 sheets defined 57.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 393 through 400 removed outlier: 3.719A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 414 No H-bonds generated for 'chain 'A' and resid 411 through 414' 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 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 489 through 492 Processing helix chain 'A' and resid 507 through 516 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 620 removed outlier: 3.618A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG A 620 " --> pdb=" O TRP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 643 removed outlier: 5.914A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 659 Processing helix chain 'A' and resid 661 through 668 removed outlier: 3.712A 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 696 Processing helix chain 'A' and resid 707 through 714 removed outlier: 5.466A pdb=" N TYR A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 725 removed outlier: 3.814A pdb=" N CYS A 721 " --> pdb=" O ARG A 718 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 773 removed outlier: 4.104A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.702A 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 827 removed outlier: 3.555A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N SER A 808 " --> pdb=" O ILE A 804 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N LEU A 809 " --> pdb=" O SER A 805 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N SER A 810 " --> pdb=" O TRP A 806 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 831 through 855 Processing helix chain 'A' and resid 862 through 891 Processing helix chain 'A' and resid 909 through 931 Processing helix chain 'A' and resid 936 through 940 removed outlier: 3.734A pdb=" N LEU A 939 " --> pdb=" O TRP A 936 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N THR A 940 " --> pdb=" O HIS A 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 936 through 940' Processing helix chain 'A' and resid 942 through 954 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 956 through 962 Processing helix chain 'A' and resid 998 through 1011 removed outlier: 3.714A pdb=" N VAL A1011 " --> pdb=" O LYS A1007 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1059 removed outlier: 3.534A pdb=" N VAL A1043 " --> pdb=" O VAL A1039 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE A1044 " --> pdb=" O ARG A1040 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE A1054 " --> pdb=" O THR A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1074 Processing helix chain 'A' and resid 1092 through 1124 removed outlier: 3.518A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 400 removed outlier: 3.719A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 414 No H-bonds generated for 'chain 'B' and resid 411 through 414' 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 436 through 438 No H-bonds generated for 'chain 'B' and resid 436 through 438' Processing helix chain 'B' and resid 459 through 477 Processing helix chain 'B' and resid 489 through 492 Processing helix chain 'B' and resid 507 through 516 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 620 removed outlier: 3.619A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ARG B 620 " --> pdb=" O TRP B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 643 removed outlier: 5.912A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 659 Processing helix chain 'B' and resid 661 through 668 removed outlier: 3.712A 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 696 Processing helix chain 'B' and resid 707 through 714 removed outlier: 5.466A pdb=" N TYR B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU B 714 " --> pdb=" O SER B 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 717 through 725 removed outlier: 3.814A pdb=" N CYS B 721 " --> pdb=" O ARG B 718 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 773 removed outlier: 4.104A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.701A 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 827 removed outlier: 3.555A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER B 808 " --> pdb=" O ILE B 804 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LEU B 809 " --> pdb=" O SER B 805 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N SER B 810 " --> pdb=" O TRP B 806 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 831 through 855 Processing helix chain 'B' and resid 862 through 891 Processing helix chain 'B' and resid 909 through 931 Processing helix chain 'B' and resid 936 through 940 removed outlier: 3.733A pdb=" N LEU B 939 " --> pdb=" O TRP B 936 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N THR B 940 " --> pdb=" O HIS B 937 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 936 through 940' Processing helix chain 'B' and resid 942 through 954 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 956 through 962 Processing helix chain 'B' and resid 998 through 1011 removed outlier: 3.714A pdb=" N VAL B1011 " --> pdb=" O LYS B1007 " (cutoff:3.500A) Processing helix chain 'B' and resid 1028 through 1059 removed outlier: 3.532A pdb=" N VAL B1043 " --> pdb=" O VAL B1039 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ILE B1044 " --> pdb=" O ARG B1040 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE B1054 " --> pdb=" O THR B1050 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1074 Processing helix chain 'B' and resid 1092 through 1124 removed outlier: 3.518A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 386 through 390 removed outlier: 7.372A pdb=" N PHE A 415 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N THR A 541 " --> pdb=" O PHE A 415 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN A 566 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 597 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL A 451 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N THR A 599 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR A 453 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU A 601 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE A 733 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA A 627 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS A 735 " --> pdb=" O ALA A 627 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY A 629 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N CYS A 737 " --> pdb=" O GLY A 629 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 630 through 633 Processing sheet with id= C, first strand: chain 'A' and resid 545 through 549 removed outlier: 6.553A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 386 through 390 removed outlier: 7.373A pdb=" N PHE B 415 " --> pdb=" O THR B 541 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR B 541 " --> pdb=" O PHE B 415 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N GLN B 566 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 597 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL B 451 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N THR B 599 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N THR B 453 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.389A pdb=" N LEU B 601 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N ILE B 733 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ALA B 627 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N LYS B 735 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLY B 629 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N CYS B 737 " --> pdb=" O GLY B 629 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 630 through 633 Processing sheet with id= F, first strand: chain 'B' and resid 545 through 549 removed outlier: 6.551A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1686 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: 3.35 Time building geometry restraints manager: 4.49 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: 1686 1.31 - 1.43: 3265 1.43 - 1.56: 6244 1.56 - 1.68: 28 1.68 - 1.81: 100 Bond restraints: 11323 Sorted by residual: bond pdb=" C31 POV A1301 " pdb=" O31 POV A1301 " ideal model delta sigma weight residual 1.327 1.438 -0.111 2.00e-02 2.50e+03 3.08e+01 bond pdb=" C31 POV B1301 " pdb=" O31 POV B1301 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.01e+01 bond pdb=" C21 POV B1301 " pdb=" O21 POV B1301 " ideal model delta sigma weight residual 1.330 1.413 -0.083 2.00e-02 2.50e+03 1.73e+01 bond pdb=" C21 POV A1301 " pdb=" O21 POV A1301 " ideal model delta sigma weight residual 1.330 1.412 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb="C312 POV A1301 " pdb="C313 POV A1301 " ideal model delta sigma weight residual 1.523 1.599 -0.076 2.00e-02 2.50e+03 1.46e+01 ... (remaining 11318 not shown) Histogram of bond angle deviations from ideal: 98.42 - 105.55: 146 105.55 - 112.68: 5926 112.68 - 119.81: 3768 119.81 - 126.94: 5394 126.94 - 134.07: 120 Bond angle restraints: 15354 Sorted by residual: angle pdb=" N ARG B 508 " pdb=" CA ARG B 508 " pdb=" C ARG B 508 " ideal model delta sigma weight residual 112.89 107.62 5.27 1.24e+00 6.50e-01 1.81e+01 angle pdb=" N ARG A 508 " pdb=" CA ARG A 508 " pdb=" C ARG A 508 " ideal model delta sigma weight residual 112.89 107.65 5.24 1.24e+00 6.50e-01 1.78e+01 angle pdb=" CA VAL B 435 " pdb=" C VAL B 435 " pdb=" O VAL B 435 " ideal model delta sigma weight residual 121.67 117.30 4.37 1.05e+00 9.07e-01 1.73e+01 angle pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" O VAL A 435 " ideal model delta sigma weight residual 121.67 117.32 4.35 1.05e+00 9.07e-01 1.72e+01 angle pdb=" O13 POV B1301 " pdb=" P POV B1301 " pdb=" O14 POV B1301 " ideal model delta sigma weight residual 121.11 109.12 11.99 3.00e+00 1.11e-01 1.60e+01 ... (remaining 15349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.62: 6309 25.62 - 51.25: 246 51.25 - 76.87: 58 76.87 - 102.50: 6 102.50 - 128.12: 2 Dihedral angle restraints: 6621 sinusoidal: 2481 harmonic: 4140 Sorted by residual: dihedral pdb=" CA ALA A 715 " pdb=" C ALA A 715 " pdb=" N GLU A 716 " pdb=" CA GLU A 716 " ideal model delta harmonic sigma weight residual -180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ALA B 715 " pdb=" C ALA B 715 " pdb=" N GLU B 716 " pdb=" CA GLU B 716 " ideal model delta harmonic sigma weight residual -180.00 -152.43 -27.57 0 5.00e+00 4.00e-02 3.04e+01 dihedral pdb=" CA TYR B 827 " pdb=" C TYR B 827 " pdb=" N HIS B 828 " pdb=" CA HIS B 828 " ideal model delta harmonic sigma weight residual 180.00 154.81 25.19 0 5.00e+00 4.00e-02 2.54e+01 ... (remaining 6618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1127 0.044 - 0.088: 479 0.088 - 0.132: 115 0.132 - 0.177: 23 0.177 - 0.221: 7 Chirality restraints: 1751 Sorted by residual: chirality pdb=" CA VAL B 435 " pdb=" N VAL B 435 " pdb=" C VAL B 435 " pdb=" CB VAL B 435 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.22e+00 chirality pdb=" CA VAL A 435 " pdb=" N VAL A 435 " pdb=" C VAL A 435 " pdb=" CB VAL A 435 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" C2 POV B1301 " pdb=" C1 POV B1301 " pdb=" C3 POV B1301 " pdb=" O21 POV B1301 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1748 not shown) Planarity restraints: 1886 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 504 " -0.017 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C LYS A 504 " 0.056 2.00e-02 2.50e+03 pdb=" O LYS A 504 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE A 505 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 504 " 0.017 2.00e-02 2.50e+03 3.25e-02 1.05e+01 pdb=" C LYS B 504 " -0.056 2.00e-02 2.50e+03 pdb=" O LYS B 504 " 0.021 2.00e-02 2.50e+03 pdb=" N ILE B 505 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A1015 " -0.025 2.00e-02 2.50e+03 2.09e-02 7.65e+00 pdb=" CG PHE A1015 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A1015 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A1015 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A1015 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A1015 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A1015 " -0.010 2.00e-02 2.50e+03 ... (remaining 1883 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2646 2.79 - 3.32: 10441 3.32 - 3.84: 18034 3.84 - 4.37: 21637 4.37 - 4.90: 37470 Nonbonded interactions: 90228 Sorted by model distance: nonbonded pdb=" NH1 ARG B 817 " pdb=" O13 POV B1301 " model vdw 2.259 2.520 nonbonded pdb=" NH1 ARG A 817 " pdb=" O13 POV A1301 " model vdw 2.260 2.520 nonbonded pdb=" OG1 THR A 394 " pdb=" NE2 GLN B1002 " model vdw 2.273 2.520 nonbonded pdb=" NE2 GLN A1002 " pdb=" OG1 THR B 394 " model vdw 2.311 2.520 nonbonded pdb=" OG SER B 611 " pdb=" O TYR B 741 " model vdw 2.318 2.440 ... (remaining 90223 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' selection = (chain 'B' and ((resid 375 and (name CA or name C or name O or name CB or name C \ G1 or name CG2 or name CD1)) or resid 376 through 1125 or resid 1301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 2.900 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.680 Find NCS groups from input model: 0.580 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: 0.000 Load rotamer database and sin/cos tables:3.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 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 : 0.008 0.111 11323 Z= 0.509 Angle : 0.864 11.988 15354 Z= 0.479 Chirality : 0.052 0.221 1751 Planarity : 0.005 0.057 1886 Dihedral : 14.850 128.121 3943 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.92 % Allowed : 0.52 % Favored : 97.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1380 helix: 1.35 (0.19), residues: 752 sheet: -0.22 (0.39), residues: 166 loop : -1.05 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A1103 HIS 0.006 0.002 HIS B 459 PHE 0.047 0.003 PHE B1015 TYR 0.024 0.003 TYR B 827 ARG 0.007 0.001 ARG B1040 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 310 time to evaluate : 1.102 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 799 PHE cc_start: 0.8588 (t80) cc_final: 0.8366 (t80) REVERT: B 799 PHE cc_start: 0.8604 (t80) cc_final: 0.8401 (t80) outliers start: 22 outliers final: 0 residues processed: 324 average time/residue: 0.2804 time to fit residues: 121.9008 Evaluate side-chains 121 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 6.9990 chunk 58 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 71 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 109 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 540 HIS A 548 ASN A 689 GLN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 540 HIS B 548 ASN B 689 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 11323 Z= 0.245 Angle : 0.565 8.505 15354 Z= 0.297 Chirality : 0.042 0.168 1751 Planarity : 0.004 0.050 1886 Dihedral : 9.619 115.521 1586 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.62 % Allowed : 11.37 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.23), residues: 1380 helix: 1.92 (0.19), residues: 744 sheet: 0.12 (0.43), residues: 145 loop : -0.87 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1047 HIS 0.011 0.002 HIS B 540 PHE 0.021 0.002 PHE A 911 TYR 0.023 0.002 TYR A 827 ARG 0.003 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 149 time to evaluate : 1.189 Fit side-chains revert: symmetry clash REVERT: A 387 PHE cc_start: 0.7712 (t80) cc_final: 0.7428 (t80) REVERT: A 601 LEU cc_start: 0.7042 (OUTLIER) cc_final: 0.6697 (mp) REVERT: B 387 PHE cc_start: 0.7688 (t80) cc_final: 0.7380 (t80) REVERT: B 601 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6792 (mp) REVERT: B 828 HIS cc_start: 0.5889 (m90) cc_final: 0.5622 (m-70) REVERT: B 876 MET cc_start: 0.7659 (tpp) cc_final: 0.7351 (tpt) REVERT: B 945 TYR cc_start: 0.8436 (t80) cc_final: 0.8225 (t80) outliers start: 30 outliers final: 16 residues processed: 172 average time/residue: 0.1958 time to fit residues: 50.9525 Evaluate side-chains 136 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 453 THR Chi-restraints excluded: chain A residue 499 SER Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 794 GLU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 1114 ILE Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 554 VAL Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1091 THR Chi-restraints excluded: chain B residue 1114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 40.0000 chunk 39 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 86 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 chunk 127 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 43 optimal weight: 0.4980 chunk 102 optimal weight: 0.0000 overall best weight: 0.8986 ------------------------------------------------------------------------------- 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: 0.7387 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11323 Z= 0.149 Angle : 0.495 6.684 15354 Z= 0.258 Chirality : 0.040 0.154 1751 Planarity : 0.004 0.048 1886 Dihedral : 8.466 91.137 1586 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.22 % Allowed : 13.04 % Favored : 85.74 % 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: 1.58 (0.23), residues: 1380 helix: 2.32 (0.19), residues: 753 sheet: 0.43 (0.44), residues: 136 loop : -0.83 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 806 HIS 0.004 0.001 HIS A 828 PHE 0.023 0.001 PHE B 799 TYR 0.024 0.001 TYR A 827 ARG 0.005 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 1.402 Fit side-chains revert: symmetry clash REVERT: A 387 PHE cc_start: 0.7683 (t80) cc_final: 0.7475 (t80) REVERT: A 556 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6863 (mt) REVERT: A 760 TRP cc_start: 0.7515 (m-10) cc_final: 0.7144 (m-10) REVERT: A 876 MET cc_start: 0.7685 (tpp) cc_final: 0.7466 (tpt) REVERT: B 387 PHE cc_start: 0.7687 (t80) cc_final: 0.7475 (t80) REVERT: B 760 TRP cc_start: 0.7502 (m-10) cc_final: 0.7146 (m-10) REVERT: B 828 HIS cc_start: 0.5632 (m90) cc_final: 0.5412 (m-70) outliers start: 14 outliers final: 7 residues processed: 141 average time/residue: 0.2043 time to fit residues: 44.1580 Evaluate side-chains 122 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 THR Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain B residue 794 GLU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.5980 chunk 14 optimal weight: 20.0000 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 135 optimal weight: 6.9990 chunk 121 optimal weight: 7.9990 chunk 36 optimal weight: 0.0050 chunk 112 optimal weight: 4.9990 overall best weight: 3.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN B 545 ASN B 650 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 11323 Z= 0.386 Angle : 0.629 6.967 15354 Z= 0.331 Chirality : 0.044 0.155 1751 Planarity : 0.004 0.042 1886 Dihedral : 8.942 101.499 1586 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.62 % Allowed : 14.87 % Favored : 82.50 % 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: 1.29 (0.23), residues: 1380 helix: 2.05 (0.18), residues: 738 sheet: 0.29 (0.41), residues: 158 loop : -0.84 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 806 HIS 0.007 0.002 HIS A 828 PHE 0.022 0.002 PHE A 772 TYR 0.018 0.002 TYR B1028 ARG 0.005 0.001 ARG A 464 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 131 time to evaluate : 1.227 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 556 LEU cc_start: 0.7155 (OUTLIER) cc_final: 0.6815 (mt) REVERT: A 760 TRP cc_start: 0.7785 (m-10) cc_final: 0.7512 (m-10) REVERT: B 601 LEU cc_start: 0.7384 (OUTLIER) cc_final: 0.6969 (mp) REVERT: B 760 TRP cc_start: 0.7771 (m-10) cc_final: 0.7497 (m-10) outliers start: 30 outliers final: 11 residues processed: 154 average time/residue: 0.1776 time to fit residues: 42.8733 Evaluate side-chains 124 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 111 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 453 THR Chi-restraints excluded: chain B residue 499 SER Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 821 VAL Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 0.0020 chunk 1 optimal weight: 7.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 34 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 overall best weight: 1.3794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 545 ASN A 937 HIS ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 937 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11323 Z= 0.184 Angle : 0.528 9.162 15354 Z= 0.271 Chirality : 0.040 0.202 1751 Planarity : 0.004 0.046 1886 Dihedral : 8.134 84.152 1586 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.75 % Allowed : 15.66 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.23), residues: 1380 helix: 2.31 (0.19), residues: 746 sheet: 0.53 (0.43), residues: 147 loop : -0.81 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 806 HIS 0.009 0.001 HIS B 828 PHE 0.016 0.001 PHE A 799 TYR 0.017 0.001 TYR B 827 ARG 0.002 0.000 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 137 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8838 (mp) REVERT: A 455 TYR cc_start: 0.8263 (t80) cc_final: 0.8015 (t80) REVERT: A 556 LEU cc_start: 0.6989 (OUTLIER) cc_final: 0.6726 (mt) REVERT: B 556 LEU cc_start: 0.7236 (OUTLIER) cc_final: 0.6900 (mt) REVERT: B 601 LEU cc_start: 0.7349 (OUTLIER) cc_final: 0.7001 (mp) REVERT: B 760 TRP cc_start: 0.7662 (m-10) cc_final: 0.7460 (m-10) REVERT: B 1040 ARG cc_start: 0.8424 (OUTLIER) cc_final: 0.8038 (ttt180) outliers start: 20 outliers final: 8 residues processed: 154 average time/residue: 0.2186 time to fit residues: 50.0285 Evaluate side-chains 136 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 135 optimal weight: 4.9990 chunk 112 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 11 optimal weight: 0.0770 chunk 44 optimal weight: 0.0670 chunk 71 optimal weight: 8.9990 chunk 130 optimal weight: 5.9990 overall best weight: 2.6282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 536 HIS ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 828 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.4576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11323 Z= 0.289 Angle : 0.567 8.333 15354 Z= 0.292 Chirality : 0.042 0.270 1751 Planarity : 0.004 0.047 1886 Dihedral : 8.368 86.401 1586 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.36 % Allowed : 16.19 % Favored : 81.45 % 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: 1.43 (0.23), residues: 1380 helix: 2.22 (0.19), residues: 740 sheet: 0.27 (0.40), residues: 158 loop : -0.86 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 806 HIS 0.010 0.001 HIS B 828 PHE 0.027 0.002 PHE B 387 TYR 0.016 0.001 TYR B 827 ARG 0.006 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 448 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8875 (mp) REVERT: A 556 LEU cc_start: 0.7023 (OUTLIER) cc_final: 0.6717 (mp) REVERT: A 760 TRP cc_start: 0.7710 (m-10) cc_final: 0.7478 (m-10) REVERT: B 556 LEU cc_start: 0.7102 (OUTLIER) cc_final: 0.6804 (mt) REVERT: B 601 LEU cc_start: 0.7374 (OUTLIER) cc_final: 0.6994 (mp) REVERT: B 1040 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8158 (ttt180) outliers start: 27 outliers final: 14 residues processed: 156 average time/residue: 0.1975 time to fit residues: 46.5202 Evaluate side-chains 146 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 554 VAL Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 601 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 76 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 419 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 HIS B 828 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 11323 Z= 0.474 Angle : 0.681 9.785 15354 Z= 0.355 Chirality : 0.045 0.178 1751 Planarity : 0.004 0.048 1886 Dihedral : 9.346 107.894 1586 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.97 % Allowed : 17.59 % Favored : 79.44 % 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: 0.80 (0.23), residues: 1380 helix: 1.64 (0.18), residues: 751 sheet: -0.04 (0.41), residues: 158 loop : -1.09 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 806 HIS 0.014 0.002 HIS B 828 PHE 0.021 0.002 PHE A1052 TYR 0.022 0.002 TYR B 945 ARG 0.005 0.001 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 126 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 523 PHE cc_start: 0.4615 (OUTLIER) cc_final: 0.3583 (p90) REVERT: A 556 LEU cc_start: 0.7035 (OUTLIER) cc_final: 0.6726 (mp) REVERT: A 601 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7574 (mp) REVERT: A 760 TRP cc_start: 0.7799 (m-10) cc_final: 0.7598 (m-10) REVERT: B 523 PHE cc_start: 0.4615 (OUTLIER) cc_final: 0.3418 (p90) REVERT: B 556 LEU cc_start: 0.7252 (OUTLIER) cc_final: 0.6906 (mt) outliers start: 34 outliers final: 18 residues processed: 152 average time/residue: 0.1882 time to fit residues: 44.3215 Evaluate side-chains 137 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 114 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 ASN Chi-restraints excluded: chain A residue 494 VAL Chi-restraints excluded: chain A residue 523 PHE Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 VAL Chi-restraints excluded: chain A residue 828 HIS Chi-restraints excluded: chain A residue 887 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 494 VAL Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 646 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 887 SER Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 106 optimal weight: 5.9990 chunk 122 optimal weight: 9.9990 chunk 129 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 419 GLN B 529 ASN B 828 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.5103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11323 Z= 0.228 Angle : 0.560 9.591 15354 Z= 0.286 Chirality : 0.041 0.195 1751 Planarity : 0.004 0.050 1886 Dihedral : 8.642 90.402 1586 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.31 % Allowed : 19.86 % Favored : 78.83 % 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: 1.14 (0.23), residues: 1380 helix: 2.00 (0.19), residues: 751 sheet: -0.03 (0.42), residues: 145 loop : -1.01 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.010 0.001 HIS B 828 PHE 0.028 0.002 PHE A 387 TYR 0.021 0.001 TYR A 945 ARG 0.004 0.000 ARG B 594 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 132 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 556 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6600 (mp) REVERT: B 556 LEU cc_start: 0.7070 (OUTLIER) cc_final: 0.6760 (mt) REVERT: B 1040 ARG cc_start: 0.8398 (OUTLIER) cc_final: 0.8098 (ttt180) outliers start: 15 outliers final: 8 residues processed: 143 average time/residue: 0.2086 time to fit residues: 45.4223 Evaluate side-chains 135 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 124 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.6980 chunk 125 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 75 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11323 Z= 0.199 Angle : 0.552 9.496 15354 Z= 0.280 Chirality : 0.041 0.280 1751 Planarity : 0.004 0.050 1886 Dihedral : 8.223 89.845 1586 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.49 % Allowed : 19.86 % Favored : 78.65 % 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: 1.25 (0.23), residues: 1380 helix: 2.10 (0.19), residues: 755 sheet: 0.11 (0.42), residues: 140 loop : -1.04 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 806 HIS 0.004 0.001 HIS B 828 PHE 0.026 0.001 PHE A 800 TYR 0.017 0.001 TYR B 945 ARG 0.007 0.000 ARG A 594 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 134 time to evaluate : 1.264 Fit side-chains revert: symmetry clash REVERT: A 556 LEU cc_start: 0.6874 (OUTLIER) cc_final: 0.6614 (mp) REVERT: B 523 PHE cc_start: 0.4659 (OUTLIER) cc_final: 0.3943 (p90) REVERT: B 556 LEU cc_start: 0.7003 (OUTLIER) cc_final: 0.6695 (mt) REVERT: B 886 MET cc_start: 0.7236 (mmt) cc_final: 0.7036 (mmm) REVERT: B 1040 ARG cc_start: 0.8410 (OUTLIER) cc_final: 0.8086 (ttt180) outliers start: 17 outliers final: 9 residues processed: 147 average time/residue: 0.1873 time to fit residues: 42.3094 Evaluate side-chains 140 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1040 ARG Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 5.9990 chunk 63 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 139 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 118 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 11323 Z= 0.151 Angle : 0.547 10.192 15354 Z= 0.273 Chirality : 0.041 0.285 1751 Planarity : 0.004 0.050 1886 Dihedral : 7.820 87.173 1586 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.05 % Allowed : 20.47 % Favored : 78.48 % 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: 1.41 (0.23), residues: 1380 helix: 2.23 (0.19), residues: 753 sheet: 0.18 (0.43), residues: 138 loop : -0.95 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 760 HIS 0.002 0.001 HIS B 965 PHE 0.028 0.001 PHE B 387 TYR 0.021 0.001 TYR A 945 ARG 0.007 0.000 ARG A 594 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 135 time to evaluate : 1.179 Fit side-chains revert: symmetry clash REVERT: A 886 MET cc_start: 0.8098 (OUTLIER) cc_final: 0.7857 (mmt) REVERT: B 523 PHE cc_start: 0.4603 (OUTLIER) cc_final: 0.4061 (p90) REVERT: B 556 LEU cc_start: 0.6992 (OUTLIER) cc_final: 0.6689 (mt) REVERT: B 612 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7253 (mt) REVERT: B 760 TRP cc_start: 0.7559 (m-10) cc_final: 0.7170 (m100) outliers start: 12 outliers final: 5 residues processed: 144 average time/residue: 0.1860 time to fit residues: 41.6457 Evaluate side-chains 134 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 793 VAL Chi-restraints excluded: chain A residue 886 MET Chi-restraints excluded: chain B residue 382 ASN Chi-restraints excluded: chain B residue 523 PHE Chi-restraints excluded: chain B residue 556 LEU Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 793 VAL Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1091 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 111 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 10.0000 chunk 14 optimal weight: 0.0980 chunk 20 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 832 ASN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.157477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.125693 restraints weight = 18823.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.129253 restraints weight = 10007.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.131539 restraints weight = 6851.666| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11323 Z= 0.187 Angle : 0.543 10.352 15354 Z= 0.275 Chirality : 0.040 0.150 1751 Planarity : 0.004 0.050 1886 Dihedral : 7.880 87.375 1586 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.96 % Allowed : 21.26 % Favored : 77.78 % 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: 1.41 (0.23), residues: 1380 helix: 2.20 (0.19), residues: 754 sheet: 0.22 (0.43), residues: 138 loop : -0.91 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 760 HIS 0.003 0.001 HIS B 828 PHE 0.044 0.001 PHE A 652 TYR 0.019 0.001 TYR A 455 ARG 0.006 0.000 ARG A 594 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2132.12 seconds wall clock time: 43 minutes 46.61 seconds (2626.61 seconds total)