Starting phenix.real_space_refine (version: 1.21rc1) on Thu Oct 5 16:44:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/10_2023/8k3r_36857_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/10_2023/8k3r_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_36857/10_2023/8k3r_36857.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/10_2023/8k3r_36857.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/10_2023/8k3r_36857_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3r_36857/10_2023/8k3r_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-1.21rc1-5097/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: 6.03, per 1000 atoms: 0.55 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: 3.99 Conformation dependent library (CDL) restraints added in 1.7 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: 2.05 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: 3.42 Time building geometry restraints manager: 4.37 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: 6299 25.62 - 51.25: 244 51.25 - 76.87: 58 76.87 - 102.50: 6 102.50 - 128.12: 2 Dihedral angle restraints: 6609 sinusoidal: 2469 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 6606 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: 0.440 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: 2.840 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 31.180 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.130 ------------------------------------------------------------------------------- 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 : 14.819 128.121 3931 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 *********************** 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 : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 0 residues processed: 324 average time/residue: 0.2752 time to fit residues: 120.3202 Evaluate side-chains 121 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7214 ------------------------------------------------------------------------------- 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: 2.9990 chunk 42 optimal weight: 4.9990 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 2.9990 chunk 127 optimal weight: 6.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7454 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 11323 Z= 0.307 Angle : 0.596 8.672 15354 Z= 0.314 Chirality : 0.043 0.169 1751 Planarity : 0.004 0.049 1886 Dihedral : 9.599 114.989 1574 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.54 % Allowed : 11.37 % Favored : 86.09 % 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: 1.07 (0.22), residues: 1380 helix: 1.84 (0.18), residues: 738 sheet: 0.18 (0.41), residues: 154 loop : -0.86 (0.28), residues: 488 *********************** 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 172 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.148 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 16 residues processed: 165 average time/residue: 0.1853 time to fit residues: 47.0191 Evaluate side-chains 133 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 117 time to evaluate : 1.190 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.1022 time to fit residues: 4.6616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 70 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 chunk 105 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 126 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 102 optimal weight: 0.4980 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 472 ASN ** B 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 11323 Z= 0.144 Angle : 0.506 8.419 15354 Z= 0.261 Chirality : 0.040 0.153 1751 Planarity : 0.004 0.048 1886 Dihedral : 8.265 85.386 1574 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.61 % Allowed : 12.60 % Favored : 86.79 % 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: 1.53 (0.23), residues: 1380 helix: 2.32 (0.19), residues: 751 sheet: 0.46 (0.45), residues: 136 loop : -0.92 (0.27), residues: 493 *********************** 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 143 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 136 time to evaluate : 1.281 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 140 average time/residue: 0.2091 time to fit residues: 44.2279 Evaluate side-chains 119 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 117 time to evaluate : 1.388 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1648 time to fit residues: 2.8543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.0370 chunk 60 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 127 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 121 optimal weight: 8.9990 chunk 36 optimal weight: 0.2980 chunk 112 optimal weight: 0.9990 overall best weight: 2.2664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 650 GLN B 650 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11323 Z= 0.264 Angle : 0.564 9.359 15354 Z= 0.289 Chirality : 0.042 0.240 1751 Planarity : 0.004 0.042 1886 Dihedral : 8.239 85.664 1574 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 1.49 % Allowed : 15.31 % Favored : 83.20 % 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: 1.53 (0.23), residues: 1380 helix: 2.29 (0.19), residues: 745 sheet: 0.56 (0.44), residues: 145 loop : -0.88 (0.28), residues: 490 *********************** 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 146 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 4 residues processed: 142 average time/residue: 0.2000 time to fit residues: 43.1335 Evaluate side-chains 115 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 111 time to evaluate : 1.256 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1012 time to fit residues: 2.4867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 93 optimal weight: 0.9990 chunk 0 optimal weight: 30.0000 chunk 69 optimal weight: 9.9990 chunk 121 optimal weight: 9.9990 chunk 34 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 536 HIS A 545 ASN A 937 HIS B 545 ASN B 937 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 11323 Z= 0.412 Angle : 0.638 7.828 15354 Z= 0.334 Chirality : 0.044 0.158 1751 Planarity : 0.004 0.045 1886 Dihedral : 9.250 103.358 1574 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 1.49 % Allowed : 16.10 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.23), residues: 1380 helix: 1.95 (0.18), residues: 740 sheet: 0.15 (0.40), residues: 158 loop : -1.04 (0.28), residues: 482 *********************** 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 150 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 133 time to evaluate : 1.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 6 residues processed: 146 average time/residue: 0.1922 time to fit residues: 42.9879 Evaluate side-chains 126 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 120 time to evaluate : 1.208 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1822 time to fit residues: 3.3265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 121 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 112 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 6.9990 chunk 71 optimal weight: 30.0000 chunk 130 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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** B 419 GLN ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 536 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11323 Z= 0.251 Angle : 0.554 10.480 15354 Z= 0.285 Chirality : 0.043 0.378 1751 Planarity : 0.004 0.048 1886 Dihedral : 8.844 89.532 1574 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.79 % Allowed : 17.41 % Favored : 81.80 % 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: 1.37 (0.23), residues: 1380 helix: 2.19 (0.19), residues: 745 sheet: 0.21 (0.41), residues: 158 loop : -0.95 (0.29), residues: 477 *********************** 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 143 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 140 average time/residue: 0.1921 time to fit residues: 41.5693 Evaluate side-chains 126 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 124 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1030 time to fit residues: 1.9099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 chunk 98 optimal weight: 7.9990 chunk 76 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 75 optimal weight: 0.9980 chunk 134 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 82 optimal weight: 30.0000 chunk 62 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11323 Z= 0.385 Angle : 0.629 9.996 15354 Z= 0.327 Chirality : 0.044 0.239 1751 Planarity : 0.004 0.048 1886 Dihedral : 9.345 99.252 1574 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.96 % Allowed : 18.81 % Favored : 80.23 % 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: 0.87 (0.23), residues: 1380 helix: 1.79 (0.19), residues: 749 sheet: 0.03 (0.43), residues: 147 loop : -1.20 (0.28), residues: 484 *********************** 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 137 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 1.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 133 average time/residue: 0.1807 time to fit residues: 37.7264 Evaluate side-chains 124 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 118 time to evaluate : 1.167 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0995 time to fit residues: 2.7350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 0.6980 chunk 85 optimal weight: 20.0000 chunk 91 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 0.1980 chunk 106 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 129 optimal weight: 20.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.5096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11323 Z= 0.179 Angle : 0.528 9.361 15354 Z= 0.270 Chirality : 0.040 0.171 1751 Planarity : 0.004 0.050 1886 Dihedral : 8.368 86.583 1574 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.35 % Allowed : 20.73 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1380 helix: 2.14 (0.19), residues: 755 sheet: 0.19 (0.43), residues: 140 loop : -1.06 (0.29), residues: 485 *********************** 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 145 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 141 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 143 average time/residue: 0.1901 time to fit residues: 42.8895 Evaluate side-chains 126 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 126 time to evaluate : 1.337 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.9990 chunk 125 optimal weight: 0.7980 chunk 129 optimal weight: 20.0000 chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 6.9990 chunk 98 optimal weight: 7.9990 chunk 38 optimal weight: 6.9990 chunk 113 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.5237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 11323 Z= 0.152 Angle : 0.534 10.027 15354 Z= 0.272 Chirality : 0.040 0.215 1751 Planarity : 0.004 0.050 1886 Dihedral : 7.846 82.250 1574 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.17 % Allowed : 21.70 % Favored : 78.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.24), residues: 1380 helix: 2.32 (0.19), residues: 750 sheet: 0.35 (0.43), residues: 140 loop : -1.03 (0.29), residues: 490 *********************** 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 137 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 135 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.1798 time to fit residues: 39.5376 Evaluate side-chains 129 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 128 time to evaluate : 1.243 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.2093 time to fit residues: 2.5821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 81 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 8.9990 chunk 128 optimal weight: 0.0870 chunk 111 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 118 optimal weight: 7.9990 overall best weight: 0.9764 ------------------------------------------------------------------------------- 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** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 828 HIS B 832 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.5300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 11323 Z= 0.160 Angle : 0.550 10.173 15354 Z= 0.275 Chirality : 0.040 0.207 1751 Planarity : 0.004 0.050 1886 Dihedral : 7.625 78.548 1574 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 22.75 % Favored : 77.25 % 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: 1.53 (0.23), residues: 1380 helix: 2.31 (0.19), residues: 752 sheet: 0.51 (0.44), residues: 140 loop : -0.96 (0.29), residues: 488 ********************** 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 127 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1734 time to fit residues: 35.1334 Evaluate side-chains 121 residues out of total 1276 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 1.192 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 0.6980 chunk 102 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 30 optimal weight: 0.1980 chunk 111 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 114 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 overall best weight: 1.7782 ------------------------------------------------------------------------------- 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** ** B 529 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 828 HIS B 832 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.157168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.124775 restraints weight = 18903.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.128566 restraints weight = 9549.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.131066 restraints weight = 6339.957| |-----------------------------------------------------------------------------| r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11323 Z= 0.218 Angle : 0.558 10.494 15354 Z= 0.283 Chirality : 0.041 0.218 1751 Planarity : 0.004 0.049 1886 Dihedral : 7.737 78.298 1574 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.09 % Allowed : 22.57 % 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: 1.43 (0.23), residues: 1380 helix: 2.26 (0.19), residues: 750 sheet: 0.39 (0.43), residues: 140 loop : -1.00 (0.29), residues: 490 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2000.89 seconds wall clock time: 37 minutes 31.44 seconds (2251.44 seconds total)