Starting phenix.real_space_refine on Sun Apr 7 19:46:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/04_2024/8k3q_36856_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/04_2024/8k3q_36856.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/04_2024/8k3q_36856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/04_2024/8k3q_36856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/04_2024/8k3q_36856_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/04_2024/8k3q_36856_updated.pdb" } resolution = 2.6 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= -0.001 sd= 0.095 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 68 5.16 5 C 7444 2.51 5 N 1833 2.21 5 O 2018 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 254": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "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: 11365 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5630 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 75} Link IDs: {'PTRANS': 21, 'TRANS': 702} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 284 Unresolved non-hydrogen angles: 354 Unresolved non-hydrogen dihedrals: 237 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 162 Chain: "B" Number of atoms: 5639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 724, 5639 Classifications: {'peptide': 724} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 21, 'TRANS': 702} Chain breaks: 6 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 274 Unresolved non-hydrogen angles: 342 Unresolved non-hydrogen dihedrals: 227 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 1, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 8, 'PHE:plan': 4, 'GLU:plan': 10, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 157 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: 6.22, per 1000 atoms: 0.55 Number of scatterers: 11365 At special positions: 0 Unit cell: (134.62, 83.74, 118.72, 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 68 16.00 P 2 15.00 O 2018 8.00 N 1833 7.00 C 7444 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: 4.60 Conformation dependent library (CDL) restraints added in 2.2 seconds 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 60 helices and 6 sheets defined 55.2% alpha, 9.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.51 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: 3.619A 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: 5.913A 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: 5.355A pdb=" N LEU A 809 " --> pdb=" O SER A 805 " (cutoff:3.500A) removed outlier: 5.990A 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: 3.733A 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: 3.715A 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: 3.620A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG B 620 " --> pdb=" O TRP B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 643 removed outlier: 5.913A 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: 3.711A 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: 5.467A pdb=" N TYR B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.331A 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: 4.103A 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: 3.554A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) removed outlier: 3.590A 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: 4.081A 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: 3.533A 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: 7.373A 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: 3.552A 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: 7.574A 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: 6.386A 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: 7.613A pdb=" N VAL A 451 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.406A 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: 6.070A 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: 6.715A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.574A 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: 7.125A 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: 7.745A 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: 6.812A 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: 5.986A pdb=" N ALA B 627 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LYS B 735 " --> pdb=" O ALA B 627 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N GLY B 629 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 6.021A 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: 6.552A 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: 3.49 Time building geometry restraints manager: 5.03 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: 1742 1.31 - 1.43: 3355 1.43 - 1.56: 6403 1.56 - 1.68: 28 1.68 - 1.80: 104 Bond restraints: 11632 Sorted by residual: bond pdb=" C31 POV A1301 " pdb=" O31 POV A1301 " ideal model delta sigma weight residual 1.327 1.437 -0.110 2.00e-02 2.50e+03 3.03e+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 3.00e+01 bond pdb=" C21 POV B1301 " pdb=" O21 POV B1301 " ideal model delta sigma weight residual 1.330 1.412 -0.082 2.00e-02 2.50e+03 1.70e+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 B1301 " pdb="C313 POV B1301 " ideal model delta sigma weight residual 1.523 1.599 -0.076 2.00e-02 2.50e+03 1.45e+01 ... (remaining 11627 not shown) Histogram of bond angle deviations from ideal: 98.40 - 105.53: 156 105.53 - 112.66: 6033 112.66 - 119.79: 3882 119.79 - 126.92: 5582 126.92 - 134.05: 121 Bond angle restraints: 15774 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 112.89 107.63 5.26 1.24e+00 6.50e-01 1.80e+01 angle pdb=" CA VAL B 435 " pdb=" C VAL B 435 " pdb=" O VAL B 435 " ideal model delta sigma weight residual 121.67 117.28 4.39 1.05e+00 9.07e-01 1.75e+01 angle pdb=" CA VAL A 435 " pdb=" C VAL A 435 " pdb=" O VAL A 435 " ideal model delta sigma weight residual 121.67 117.29 4.38 1.05e+00 9.07e-01 1.74e+01 angle pdb=" O13 POV B1301 " pdb=" P POV B1301 " pdb=" O14 POV B1301 " ideal model delta sigma weight residual 121.11 109.16 11.95 3.00e+00 1.11e-01 1.59e+01 ... (remaining 15769 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.63: 6484 25.63 - 51.25: 250 51.25 - 76.88: 58 76.88 - 102.51: 6 102.51 - 128.13: 2 Dihedral angle restraints: 6800 sinusoidal: 2534 harmonic: 4266 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 -152.36 -27.64 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 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+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 180.00 154.83 25.17 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 6797 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1155 0.044 - 0.089: 493 0.089 - 0.133: 114 0.133 - 0.177: 24 0.177 - 0.222: 6 Chirality restraints: 1792 Sorted by residual: 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 1.23e+00 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=" 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 2.61 -0.18 2.00e-01 2.50e+01 8.43e-01 ... (remaining 1789 not shown) Planarity restraints: 1945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 504 " -0.017 2.00e-02 2.50e+03 3.27e-02 1.07e+01 pdb=" C LYS B 504 " 0.057 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=" 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=" CB PHE B1015 " -0.025 2.00e-02 2.50e+03 2.08e-02 7.58e+00 pdb=" CG PHE B1015 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B1015 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B1015 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B1015 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B1015 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B1015 " -0.009 2.00e-02 2.50e+03 ... (remaining 1942 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2731 2.79 - 3.32: 10695 3.32 - 3.84: 18539 3.84 - 4.37: 22195 4.37 - 4.90: 38479 Nonbonded interactions: 92639 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 2.259 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 92634 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 245 through 705 or (resid 706 and (name N or name CA or na \ me C or name O or name CB )) or resid 707 through 1006 or (resid 1007 and (name \ N or name CA or name C or name O or name CB )) or resid 1008 through 1125 or res \ id 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.610 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: 7.410 Check model and map are aligned: 0.180 Set scattering table: 0.110 Process input model: 33.440 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 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 0.110 11632 Z= 0.503 Angle : 0.869 11.949 15774 Z= 0.483 Chirality : 0.051 0.222 1792 Planarity : 0.005 0.057 1945 Dihedral : 14.742 128.132 4044 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.89 % Allowed : 0.51 % Favored : 97.60 % 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: 0.38 (0.22), residues: 1420 helix: 1.35 (0.19), residues: 752 sheet: -0.21 (0.39), residues: 166 loop : -1.27 (0.27), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP B1103 HIS 0.005 0.002 HIS B 459 PHE 0.047 0.003 PHE B1015 TYR 0.036 0.003 TYR B 249 ARG 0.007 0.001 ARG A1040 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 164 time to evaluate : 1.305 Fit side-chains REVERT: A 656 MET cc_start: 0.8932 (mmt) cc_final: 0.8521 (mmt) REVERT: A 689 GLN cc_start: 0.8016 (tp40) cc_final: 0.7347 (mt0) REVERT: A 859 LYS cc_start: 0.8009 (mmtt) cc_final: 0.7682 (mppt) REVERT: A 1108 SER cc_start: 0.8412 (t) cc_final: 0.8189 (m) REVERT: B 388 ASP cc_start: 0.7920 (OUTLIER) cc_final: 0.7649 (t0) REVERT: B 594 ARG cc_start: 0.7909 (mmt180) cc_final: 0.7653 (mmp-170) REVERT: B 656 MET cc_start: 0.8861 (mmt) cc_final: 0.8394 (mmt) REVERT: B 689 GLN cc_start: 0.7923 (tp40) cc_final: 0.7338 (mt0) REVERT: B 859 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7522 (mppt) REVERT: B 875 MET cc_start: 0.8570 (ttm) cc_final: 0.8322 (mtp) outliers start: 22 outliers final: 2 residues processed: 177 average time/residue: 1.4247 time to fit residues: 270.8910 Evaluate side-chains 131 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 817 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 426 ASN A 545 ASN A 560 GLN A 650 GLN A 856 ASN A1013 ASN B 426 ASN B 545 ASN B 548 ASN B 560 GLN B 650 GLN B 706 HIS B1013 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.1385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 11632 Z= 0.239 Angle : 0.519 4.869 15774 Z= 0.279 Chirality : 0.042 0.159 1792 Planarity : 0.005 0.050 1945 Dihedral : 9.811 111.768 1643 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.72 % Allowed : 8.66 % Favored : 89.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.23), residues: 1420 helix: 1.99 (0.19), residues: 760 sheet: 0.09 (0.37), residues: 166 loop : -0.94 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B1103 HIS 0.004 0.001 HIS B 774 PHE 0.014 0.002 PHE A 708 TYR 0.017 0.002 TYR A1008 ARG 0.006 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 1.345 Fit side-chains revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6590 (m-30) cc_final: 0.6276 (m-30) REVERT: A 689 GLN cc_start: 0.8012 (tp40) cc_final: 0.7338 (mt0) REVERT: A 749 ARG cc_start: 0.7793 (mtp180) cc_final: 0.7510 (mmm-85) REVERT: A 859 LYS cc_start: 0.8037 (mmtt) cc_final: 0.7766 (mppt) REVERT: A 1090 MET cc_start: 0.7902 (ttm) cc_final: 0.7623 (ttm) REVERT: A 1108 SER cc_start: 0.8340 (t) cc_final: 0.8102 (m) REVERT: B 471 ASP cc_start: 0.6547 (m-30) cc_final: 0.6231 (m-30) REVERT: B 689 GLN cc_start: 0.7991 (tp40) cc_final: 0.7349 (mt0) REVERT: B 859 LYS cc_start: 0.7949 (mmtt) cc_final: 0.7665 (mppt) outliers start: 20 outliers final: 9 residues processed: 141 average time/residue: 1.1869 time to fit residues: 182.6595 Evaluate side-chains 130 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 121 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 982 ILE Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 72 optimal weight: 8.9990 chunk 40 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 131 optimal weight: 0.8980 chunk 141 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.4980 chunk 105 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 560 GLN A 650 GLN A1002 GLN A1013 ASN B 650 GLN B 706 HIS B1013 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 11632 Z= 0.167 Angle : 0.450 4.849 15774 Z= 0.243 Chirality : 0.040 0.162 1792 Planarity : 0.004 0.049 1945 Dihedral : 8.832 94.392 1641 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.32 % Allowed : 10.21 % Favored : 87.48 % 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: 1.50 (0.22), residues: 1420 helix: 2.25 (0.18), residues: 772 sheet: 0.40 (0.39), residues: 156 loop : -0.87 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1103 HIS 0.003 0.001 HIS A 965 PHE 0.019 0.001 PHE B 911 TYR 0.012 0.001 TYR A 827 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 133 time to evaluate : 1.340 Fit side-chains revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6561 (m-30) cc_final: 0.6239 (m-30) REVERT: A 480 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6663 (mptt) REVERT: A 689 GLN cc_start: 0.8060 (tp40) cc_final: 0.7347 (mt0) REVERT: A 749 ARG cc_start: 0.7750 (mtp180) cc_final: 0.7491 (mmm-85) REVERT: A 859 LYS cc_start: 0.8099 (mmtt) cc_final: 0.7856 (mppt) REVERT: A 875 MET cc_start: 0.8351 (mtp) cc_final: 0.8111 (ttm) REVERT: A 1002 GLN cc_start: 0.7436 (OUTLIER) cc_final: 0.7201 (tp-100) REVERT: B 471 ASP cc_start: 0.6509 (m-30) cc_final: 0.6192 (m-30) REVERT: B 689 GLN cc_start: 0.7965 (tp40) cc_final: 0.7285 (mt0) REVERT: B 859 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7783 (mppt) REVERT: B 875 MET cc_start: 0.8355 (mtp) cc_final: 0.8026 (ttm) REVERT: B 1090 MET cc_start: 0.7809 (ttm) cc_final: 0.7371 (ttm) outliers start: 27 outliers final: 13 residues processed: 147 average time/residue: 1.2006 time to fit residues: 191.7713 Evaluate side-chains 143 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 128 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 656 MET Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1002 GLN Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 656 MET Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 129 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 131 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 419 GLN A 560 GLN A 650 GLN A1013 ASN B 419 GLN B 650 GLN B 706 HIS B1013 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11632 Z= 0.253 Angle : 0.499 4.919 15774 Z= 0.267 Chirality : 0.042 0.158 1792 Planarity : 0.004 0.048 1945 Dihedral : 8.775 94.880 1640 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.32 % Allowed : 11.23 % Favored : 86.45 % 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: 1.41 (0.22), residues: 1420 helix: 2.20 (0.18), residues: 768 sheet: 0.37 (0.38), residues: 156 loop : -0.94 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 806 HIS 0.005 0.001 HIS A 828 PHE 0.020 0.002 PHE A 911 TYR 0.013 0.002 TYR A 254 ARG 0.007 0.001 ARG B 749 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.330 Fit side-chains revert: symmetry clash REVERT: A 480 LYS cc_start: 0.6996 (OUTLIER) cc_final: 0.6720 (mptt) REVERT: A 689 GLN cc_start: 0.8062 (tp40) cc_final: 0.7315 (mt0) REVERT: A 749 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7499 (mmm-85) REVERT: A 859 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7858 (mppt) REVERT: B 689 GLN cc_start: 0.8039 (tp40) cc_final: 0.7341 (mt0) REVERT: B 859 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7827 (mppt) outliers start: 27 outliers final: 12 residues processed: 149 average time/residue: 1.1680 time to fit residues: 189.8028 Evaluate side-chains 141 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 982 ILE Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 459 HIS A 548 ASN A 650 GLN ** A1002 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1013 ASN B 459 HIS B 650 GLN B 706 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11632 Z= 0.355 Angle : 0.570 6.748 15774 Z= 0.304 Chirality : 0.045 0.165 1792 Planarity : 0.005 0.047 1945 Dihedral : 9.198 99.467 1640 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.26 % Allowed : 10.55 % Favored : 86.19 % 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 (0.22), residues: 1420 helix: 2.00 (0.18), residues: 760 sheet: 0.33 (0.37), residues: 166 loop : -1.08 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 806 HIS 0.006 0.002 HIS B 828 PHE 0.022 0.002 PHE A 911 TYR 0.016 0.002 TYR A 254 ARG 0.004 0.001 ARG A 687 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 1.273 Fit side-chains REVERT: A 445 GLU cc_start: 0.7410 (OUTLIER) cc_final: 0.7128 (pp20) REVERT: A 480 LYS cc_start: 0.7006 (OUTLIER) cc_final: 0.6768 (mptt) REVERT: A 594 ARG cc_start: 0.7858 (OUTLIER) cc_final: 0.7071 (mmp80) REVERT: A 689 GLN cc_start: 0.8096 (tp40) cc_final: 0.7322 (mt0) REVERT: A 749 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7497 (mmm-85) REVERT: A 1108 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7926 (m) REVERT: B 480 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6799 (mptt) REVERT: B 594 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.7088 (mmp80) REVERT: B 1108 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7924 (m) outliers start: 38 outliers final: 12 residues processed: 159 average time/residue: 1.1735 time to fit residues: 203.4304 Evaluate side-chains 146 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 127 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 445 GLU Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 921 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 921 THR Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 46 optimal weight: 0.8980 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 139 optimal weight: 0.6980 chunk 115 optimal weight: 0.7980 chunk 64 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 134 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1002 GLN B 706 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11632 Z= 0.217 Angle : 0.481 4.939 15774 Z= 0.259 Chirality : 0.041 0.161 1792 Planarity : 0.004 0.048 1945 Dihedral : 8.639 88.569 1640 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.66 % Allowed : 12.26 % Favored : 85.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.22), residues: 1420 helix: 2.17 (0.18), residues: 772 sheet: 0.40 (0.39), residues: 156 loop : -1.06 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 779 HIS 0.006 0.001 HIS B 828 PHE 0.019 0.002 PHE B 911 TYR 0.011 0.001 TYR B1028 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 125 time to evaluate : 1.372 Fit side-chains revert: symmetry clash REVERT: A 480 LYS cc_start: 0.6844 (OUTLIER) cc_final: 0.6555 (mptt) REVERT: A 594 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7058 (mmp80) REVERT: A 689 GLN cc_start: 0.8082 (tp40) cc_final: 0.7315 (mt0) REVERT: A 749 ARG cc_start: 0.7771 (mtp180) cc_final: 0.7493 (mmm-85) outliers start: 31 outliers final: 12 residues processed: 145 average time/residue: 1.1833 time to fit residues: 187.4312 Evaluate side-chains 140 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 126 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 15 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 138 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 ASN B 706 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11632 Z= 0.227 Angle : 0.484 4.929 15774 Z= 0.261 Chirality : 0.041 0.161 1792 Planarity : 0.004 0.048 1945 Dihedral : 8.383 89.004 1640 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.74 % Allowed : 12.52 % Favored : 84.73 % 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: 1.40 (0.22), residues: 1420 helix: 2.20 (0.18), residues: 772 sheet: 0.45 (0.39), residues: 156 loop : -1.02 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 779 HIS 0.006 0.001 HIS B 828 PHE 0.020 0.002 PHE B 911 TYR 0.012 0.001 TYR A 254 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.276 Fit side-chains revert: symmetry clash REVERT: A 480 LYS cc_start: 0.6827 (OUTLIER) cc_final: 0.6538 (mptt) REVERT: A 594 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.7086 (mmp80) REVERT: A 749 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7492 (mmm-85) REVERT: B 480 LYS cc_start: 0.6944 (OUTLIER) cc_final: 0.6689 (mptt) outliers start: 32 outliers final: 14 residues processed: 149 average time/residue: 1.1543 time to fit residues: 188.2753 Evaluate side-chains 142 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 480 LYS Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 3.9990 chunk 82 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 706 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 11632 Z= 0.403 Angle : 0.590 6.169 15774 Z= 0.314 Chirality : 0.046 0.171 1792 Planarity : 0.005 0.047 1945 Dihedral : 9.086 97.931 1640 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.49 % Allowed : 12.95 % Favored : 84.56 % 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: 1.02 (0.22), residues: 1420 helix: 1.83 (0.18), residues: 774 sheet: 0.33 (0.39), residues: 156 loop : -1.11 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 806 HIS 0.009 0.002 HIS B 828 PHE 0.021 0.002 PHE B 911 TYR 0.014 0.002 TYR A 254 ARG 0.004 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 125 time to evaluate : 1.298 Fit side-chains REVERT: A 480 LYS cc_start: 0.6955 (OUTLIER) cc_final: 0.6704 (mptt) REVERT: A 594 ARG cc_start: 0.7859 (OUTLIER) cc_final: 0.7052 (mmp80) REVERT: A 749 ARG cc_start: 0.7790 (mtp180) cc_final: 0.7498 (mmm-85) REVERT: A 1108 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.7914 (m) REVERT: B 594 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7063 (mmp80) REVERT: B 1108 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7911 (m) outliers start: 29 outliers final: 14 residues processed: 147 average time/residue: 1.1417 time to fit residues: 183.5564 Evaluate side-chains 143 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 124 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 606 MET Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 388 ASP Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 594 ARG Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 132 optimal weight: 0.7980 chunk 121 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 56 optimal weight: 0.0980 chunk 101 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 116 optimal weight: 0.5980 chunk 122 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 706 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 11632 Z= 0.151 Angle : 0.451 4.873 15774 Z= 0.245 Chirality : 0.040 0.158 1792 Planarity : 0.004 0.048 1945 Dihedral : 8.222 85.373 1640 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.14 % Allowed : 13.46 % Favored : 84.39 % 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: 1.48 (0.22), residues: 1420 helix: 2.25 (0.18), residues: 774 sheet: 0.52 (0.39), residues: 156 loop : -0.99 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 779 HIS 0.004 0.001 HIS A 828 PHE 0.018 0.001 PHE B 911 TYR 0.010 0.001 TYR B 797 ARG 0.004 0.000 ARG B 687 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 121 time to evaluate : 1.383 Fit side-chains revert: symmetry clash REVERT: A 480 LYS cc_start: 0.6813 (OUTLIER) cc_final: 0.6520 (mptt) REVERT: A 594 ARG cc_start: 0.7837 (OUTLIER) cc_final: 0.7486 (mmp80) REVERT: A 749 ARG cc_start: 0.7758 (mtp180) cc_final: 0.7478 (mmm-85) outliers start: 25 outliers final: 14 residues processed: 135 average time/residue: 1.1649 time to fit residues: 172.0413 Evaluate side-chains 136 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 602 ASP Chi-restraints excluded: chain B residue 672 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 0.5980 chunk 114 optimal weight: 0.0570 chunk 11 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- 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: 0.7958 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 11632 Z= 0.163 Angle : 0.445 5.157 15774 Z= 0.241 Chirality : 0.040 0.159 1792 Planarity : 0.004 0.049 1945 Dihedral : 7.654 77.348 1640 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.54 % Allowed : 13.98 % Favored : 84.48 % 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: 1.63 (0.22), residues: 1420 helix: 2.34 (0.18), residues: 778 sheet: 0.63 (0.39), residues: 156 loop : -0.89 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 779 HIS 0.004 0.001 HIS A 828 PHE 0.016 0.001 PHE B 911 TYR 0.010 0.001 TYR B 797 ARG 0.004 0.000 ARG B 687 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2840 Ramachandran restraints generated. 1420 Oldfield, 0 Emsley, 1420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 125 time to evaluate : 1.394 Fit side-chains REVERT: A 480 LYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6553 (mptt) REVERT: A 749 ARG cc_start: 0.7737 (mtp180) cc_final: 0.7444 (mmm-85) outliers start: 18 outliers final: 11 residues processed: 137 average time/residue: 1.2445 time to fit residues: 185.6235 Evaluate side-chains 137 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 125 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 480 LYS Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 446 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1070 MET Chi-restraints excluded: chain B residue 1108 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 114 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 100 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 252 ASN B 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.138161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.108584 restraints weight = 12660.876| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 1.76 r_work: 0.3133 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11632 Z= 0.184 Angle : 0.458 5.118 15774 Z= 0.247 Chirality : 0.040 0.156 1792 Planarity : 0.004 0.048 1945 Dihedral : 7.490 81.575 1636 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 1.37 % Allowed : 13.72 % Favored : 84.91 % 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: 1.65 (0.22), residues: 1420 helix: 2.37 (0.18), residues: 774 sheet: 0.63 (0.39), residues: 156 loop : -0.88 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 779 HIS 0.005 0.001 HIS A 828 PHE 0.018 0.001 PHE B 911 TYR 0.010 0.001 TYR B 797 ARG 0.004 0.000 ARG B 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3945.04 seconds wall clock time: 71 minutes 40.58 seconds (4300.58 seconds total)