Starting phenix.real_space_refine on Sat Jul 20 18:11:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/07_2024/8k3q_36856.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/07_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_36856/07_2024/8k3q_36856.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/07_2024/8k3q_36856.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/07_2024/8k3q_36856.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3q_36856/07_2024/8k3q_36856.cif" } 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-5388/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: 6.72, per 1000 atoms: 0.59 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: 4.30 Conformation dependent library (CDL) restraints added in 2.0 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... Secondary structure from input PDB file: 66 helices and 8 sheets defined 62.6% alpha, 10.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.55 Creating SS restraints... Processing helix chain 'A' and resid 392 through 401 removed outlier: 3.610A pdb=" N LEU A 396 " --> pdb=" O SER A 392 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN A 398 " --> pdb=" O THR A 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 401 " --> pdb=" O ASP A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 removed outlier: 4.099A pdb=" N LYS A 414 " --> pdb=" O PRO A 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 410 through 414' Processing helix chain 'A' and resid 424 through 428 removed outlier: 3.968A pdb=" N LEU A 428 " --> pdb=" O PRO A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 439 Processing helix chain 'A' and resid 458 through 478 Processing helix chain 'A' and resid 488 through 491 Processing helix chain 'A' and resid 506 through 517 Processing helix chain 'A' and resid 577 through 588 Processing helix chain 'A' and resid 588 through 594 removed outlier: 3.619A pdb=" N LEU A 592 " --> pdb=" O GLY A 588 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 617 Processing helix chain 'A' and resid 618 through 621 removed outlier: 3.836A pdb=" N ASN A 621 " --> pdb=" O GLU A 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 618 through 621' Processing helix chain 'A' and resid 636 through 643 removed outlier: 3.550A pdb=" N PHE A 639 " --> pdb=" O GLY A 636 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 660 Processing helix chain 'A' and resid 660 through 669 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 687 Processing helix chain 'A' and resid 688 through 696 Processing helix chain 'A' and resid 706 through 712 Processing helix chain 'A' and resid 713 through 716 removed outlier: 3.927A pdb=" N GLU A 716 " --> pdb=" O TYR A 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 716' Processing helix chain 'A' and resid 717 through 726 removed outlier: 3.681A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 774 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 781 removed outlier: 3.622A pdb=" N SER A 781 " --> pdb=" O VAL A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 784 through 807 removed outlier: 3.555A pdb=" N PHE A 807 " --> pdb=" O LEU A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 828 removed outlier: 3.662A pdb=" N PHE A 813 " --> pdb=" O LEU A 809 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 Processing helix chain 'A' and resid 861 through 892 removed outlier: 3.906A pdb=" N TYR A 865 " --> pdb=" O THR A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 932 Processing helix chain 'A' and resid 936 through 941 Processing helix chain 'A' and resid 941 through 955 removed outlier: 3.557A pdb=" N TYR A 945 " --> pdb=" O SER A 941 " (cutoff:3.500A) Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 955 through 963 Processing helix chain 'A' and resid 997 through 1012 removed outlier: 3.715A pdb=" N VAL A1011 " --> pdb=" O LYS A1007 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU A1012 " --> pdb=" O TYR A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1060 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 1063 through 1075 Processing helix chain 'A' and resid 1091 through 1125 removed outlier: 4.100A pdb=" N SER A1095 " --> pdb=" O THR A1091 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (cutoff:3.500A) Processing helix chain 'B' and resid 392 through 401 removed outlier: 3.610A pdb=" N LEU B 396 " --> pdb=" O SER B 392 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN B 398 " --> pdb=" O THR B 394 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR B 401 " --> pdb=" O ASP B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 410 through 414 removed outlier: 4.099A pdb=" N LYS B 414 " --> pdb=" O PRO B 410 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 410 through 414' Processing helix chain 'B' and resid 424 through 428 removed outlier: 3.968A pdb=" N LEU B 428 " --> pdb=" O PRO B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 439 Processing helix chain 'B' and resid 458 through 478 Processing helix chain 'B' and resid 488 through 491 Processing helix chain 'B' and resid 506 through 517 Processing helix chain 'B' and resid 577 through 588 Processing helix chain 'B' and resid 588 through 594 removed outlier: 3.620A pdb=" N LEU B 592 " --> pdb=" O GLY B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 610 through 617 Processing helix chain 'B' and resid 618 through 621 removed outlier: 3.837A pdb=" N ASN B 621 " --> pdb=" O GLU B 618 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 618 through 621' Processing helix chain 'B' and resid 636 through 643 removed outlier: 3.550A pdb=" N PHE B 639 " --> pdb=" O GLY B 636 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) Processing helix chain 'B' and resid 644 through 660 Processing helix chain 'B' and resid 660 through 669 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 687 Processing helix chain 'B' and resid 688 through 696 Processing helix chain 'B' and resid 706 through 712 Processing helix chain 'B' and resid 713 through 716 removed outlier: 3.927A pdb=" N GLU B 716 " --> pdb=" O TYR B 713 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 713 through 716' Processing helix chain 'B' and resid 717 through 726 removed outlier: 3.681A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 774 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 781 removed outlier: 3.622A pdb=" N SER B 781 " --> pdb=" O VAL B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 784 through 807 removed outlier: 3.554A pdb=" N PHE B 807 " --> pdb=" O LEU B 803 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 828 removed outlier: 3.663A pdb=" N PHE B 813 " --> pdb=" O LEU B 809 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 856 Processing helix chain 'B' and resid 861 through 892 removed outlier: 3.906A pdb=" N TYR B 865 " --> pdb=" O THR B 861 " (cutoff:3.500A) Processing helix chain 'B' and resid 909 through 932 Processing helix chain 'B' and resid 936 through 941 Processing helix chain 'B' and resid 941 through 955 removed outlier: 3.557A pdb=" N TYR B 945 " --> pdb=" O SER B 941 " (cutoff:3.500A) Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 955 through 963 Processing helix chain 'B' and resid 997 through 1012 removed outlier: 3.714A pdb=" N VAL B1011 " --> pdb=" O LYS B1007 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N LEU B1012 " --> pdb=" O TYR B1008 " (cutoff:3.500A) Processing helix chain 'B' and resid 1027 through 1060 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 1063 through 1075 Processing helix chain 'B' and resid 1091 through 1125 removed outlier: 4.100A pdb=" N SER B1095 " --> pdb=" O THR B1091 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.798A pdb=" N ARG A 376 " --> pdb=" O MET B 992 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET B 992 " --> pdb=" O ARG A 376 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, 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: 6.812A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL A 624 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS A 735 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY A 626 " --> pdb=" O LYS A 735 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N CYS A 737 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS A 628 " --> pdb=" O CYS A 737 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N SER A 739 " --> pdb=" O CYS A 628 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU A 630 " --> pdb=" O SER A 739 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR A 741 " --> pdb=" O GLU A 630 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG A 632 " --> pdb=" O TYR A 741 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER A 743 " --> pdb=" O ARG A 632 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 531 through 532 removed outlier: 6.748A pdb=" N GLU A 527 " --> pdb=" O ILE B 982 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 545 through 549 removed outlier: 5.226A pdb=" N ILE A 546 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N GLU A 557 " --> pdb=" O ILE A 546 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ASN A 548 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 981 through 982 Processing sheet with id=AA6, first strand: chain 'A' and resid 991 through 992 removed outlier: 3.637A pdb=" N MET A 992 " --> pdb=" O ARG B 376 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG B 376 " --> pdb=" O MET A 992 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, 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: 6.812A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N VAL B 624 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 7.594A pdb=" N LYS B 735 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N GLY B 626 " --> pdb=" O LYS B 735 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N CYS B 737 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N CYS B 628 " --> pdb=" O CYS B 737 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N SER B 739 " --> pdb=" O CYS B 628 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU B 630 " --> pdb=" O SER B 739 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N TYR B 741 " --> pdb=" O GLU B 630 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARG B 632 " --> pdb=" O TYR B 741 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N SER B 743 " --> pdb=" O ARG B 632 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 545 through 549 removed outlier: 5.226A pdb=" N ILE B 546 " --> pdb=" O GLU B 557 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU B 557 " --> pdb=" O ILE B 546 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ASN B 548 " --> pdb=" O SER B 555 " (cutoff:3.500A) 679 hydrogen bonds defined for protein. 1947 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: 4.16 Time building geometry restraints manager: 4.72 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: 2727 2.79 - 3.32: 10636 3.32 - 3.84: 18482 3.84 - 4.37: 22017 4.37 - 4.90: 38437 Nonbonded interactions: 92299 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 92294 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: 1.590 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: 0.000 Extract box with map and model: 0.460 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 34.010 Find NCS groups from input model: 0.500 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: 0.000 Load rotamer database and sin/cos tables:12.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.990 ------------------------------------------------------------------------------- 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= 0.514 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 : 1.291 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: 1.3726 time to fit residues: 260.9276 Evaluate side-chains 131 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 1.348 ------------------------------------------------------------------------------- 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: 5.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 112 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 130 optimal weight: 0.8980 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 419 GLN 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: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11632 Z= 0.249 Angle : 0.539 5.586 15774 Z= 0.292 Chirality : 0.042 0.171 1792 Planarity : 0.005 0.052 1945 Dihedral : 9.939 113.978 1643 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.54 % Allowed : 8.66 % Favored : 89.79 % 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: 1.19 (0.22), residues: 1420 helix: 2.00 (0.18), residues: 782 sheet: -0.01 (0.39), residues: 156 loop : -0.96 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B1103 HIS 0.004 0.001 HIS B 774 PHE 0.014 0.002 PHE B 864 TYR 0.016 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 152 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 134 time to evaluate : 1.323 Fit side-chains revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6592 (m-30) cc_final: 0.6308 (m-30) REVERT: A 689 GLN cc_start: 0.7979 (tp40) cc_final: 0.7315 (mt0) REVERT: A 749 ARG cc_start: 0.7753 (mtp180) cc_final: 0.7486 (mmm-85) REVERT: A 859 LYS cc_start: 0.7974 (mmtt) cc_final: 0.7684 (mppt) REVERT: A 875 MET cc_start: 0.8598 (ttm) cc_final: 0.8398 (mtp) REVERT: A 1090 MET cc_start: 0.7841 (ttm) cc_final: 0.7552 (ttm) REVERT: A 1108 SER cc_start: 0.8341 (t) cc_final: 0.8107 (m) REVERT: B 471 ASP cc_start: 0.6520 (m-30) cc_final: 0.6220 (m-30) REVERT: B 689 GLN cc_start: 0.7905 (tp40) cc_final: 0.7290 (mt0) REVERT: B 859 LYS cc_start: 0.7954 (mmtt) cc_final: 0.7668 (mppt) outliers start: 18 outliers final: 8 residues processed: 145 average time/residue: 1.1597 time to fit residues: 184.7697 Evaluate side-chains 133 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 125 time to evaluate : 1.307 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 131 optimal weight: 2.9990 chunk 141 optimal weight: 0.8980 chunk 116 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 548 ASN A 560 GLN A 937 HIS A1013 ASN B 548 ASN B 650 GLN B 706 HIS B 856 ASN B1013 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7970 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11632 Z= 0.280 Angle : 0.540 5.443 15774 Z= 0.291 Chirality : 0.043 0.174 1792 Planarity : 0.005 0.044 1945 Dihedral : 9.397 102.656 1641 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.49 % Allowed : 10.46 % Favored : 87.05 % 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: 1.39 (0.22), residues: 1420 helix: 2.20 (0.18), residues: 780 sheet: 0.14 (0.38), residues: 156 loop : -0.98 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 806 HIS 0.005 0.002 HIS A 828 PHE 0.022 0.002 PHE B 911 TYR 0.015 0.002 TYR B1008 ARG 0.004 0.001 ARG B 749 *********************** 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 156 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 749 ARG cc_start: 0.7743 (mtp180) cc_final: 0.7483 (mmm-85) REVERT: A 859 LYS cc_start: 0.8031 (mmtt) cc_final: 0.7823 (mppt) REVERT: A 875 MET cc_start: 0.8580 (ttm) cc_final: 0.8369 (mtp) REVERT: B 859 LYS cc_start: 0.8073 (mmtt) cc_final: 0.7830 (mppt) REVERT: B 875 MET cc_start: 0.8406 (mtp) cc_final: 0.8174 (ttm) REVERT: B 1108 SER cc_start: 0.8309 (OUTLIER) cc_final: 0.7928 (m) outliers start: 29 outliers final: 8 residues processed: 142 average time/residue: 1.1716 time to fit residues: 181.4579 Evaluate side-chains 134 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 125 time to evaluate : 1.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 388 ASP 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 939 LEU 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: 2.9990 chunk 98 optimal weight: 0.3980 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 131 optimal weight: 3.9990 chunk 139 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 560 GLN A 650 GLN A1013 ASN B 650 GLN B 706 HIS B 937 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2132 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= 0.174 Angle : 0.462 5.100 15774 Z= 0.251 Chirality : 0.040 0.171 1792 Planarity : 0.004 0.044 1945 Dihedral : 8.517 88.452 1640 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.49 % Allowed : 11.15 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.22), residues: 1420 helix: 2.56 (0.18), residues: 776 sheet: 0.29 (0.39), residues: 156 loop : -0.88 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 779 HIS 0.003 0.001 HIS A 828 PHE 0.017 0.001 PHE A 911 TYR 0.012 0.001 TYR A 827 ARG 0.003 0.000 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 161 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6512 (m-30) cc_final: 0.6272 (m-30) REVERT: A 749 ARG cc_start: 0.7688 (mtp180) cc_final: 0.7458 (mmm-85) REVERT: B 471 ASP cc_start: 0.6493 (m-30) cc_final: 0.6250 (m-30) REVERT: B 859 LYS cc_start: 0.8039 (mmtt) cc_final: 0.7836 (mppt) outliers start: 29 outliers final: 16 residues processed: 148 average time/residue: 1.1393 time to fit residues: 184.4600 Evaluate side-chains 144 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 time to evaluate : 1.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 606 MET 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 1070 MET Chi-restraints excluded: chain A residue 1108 SER Chi-restraints excluded: chain B residue 401 THR Chi-restraints excluded: chain B residue 594 ARG 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 1108 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 115 optimal weight: 1.9990 chunk 79 optimal weight: 0.0980 chunk 2 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 96 optimal weight: 0.0770 chunk 0 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 ASN B 706 HIS B1013 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11632 Z= 0.213 Angle : 0.484 5.208 15774 Z= 0.261 Chirality : 0.041 0.168 1792 Planarity : 0.004 0.043 1945 Dihedral : 8.358 86.835 1640 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.66 % Allowed : 11.84 % Favored : 85.51 % 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: 1.77 (0.22), residues: 1420 helix: 2.57 (0.18), residues: 776 sheet: 0.30 (0.39), residues: 156 loop : -0.89 (0.27), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 806 HIS 0.004 0.001 HIS A 828 PHE 0.019 0.002 PHE B 911 TYR 0.011 0.001 TYR A 254 ARG 0.003 0.000 ARG B 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 160 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 129 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 471 ASP cc_start: 0.6562 (m-30) cc_final: 0.6304 (m-30) REVERT: A 749 ARG cc_start: 0.7699 (mtp180) cc_final: 0.7465 (mmm-85) outliers start: 31 outliers final: 15 residues processed: 147 average time/residue: 1.1596 time to fit residues: 186.1418 Evaluate side-chains 145 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 130 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 388 ASP 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 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 594 ARG 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 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: 0.6980 chunk 125 optimal weight: 5.9990 chunk 27 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 73 optimal weight: 8.9990 chunk 134 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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: 0.7978 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11632 Z= 0.264 Angle : 0.514 5.596 15774 Z= 0.277 Chirality : 0.042 0.166 1792 Planarity : 0.004 0.043 1945 Dihedral : 8.597 91.307 1640 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.74 % Allowed : 12.26 % Favored : 84.99 % 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: 1.66 (0.22), residues: 1420 helix: 2.45 (0.18), residues: 780 sheet: 0.26 (0.39), residues: 156 loop : -0.91 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 806 HIS 0.005 0.001 HIS A 828 PHE 0.019 0.002 PHE A 911 TYR 0.012 0.002 TYR A 254 ARG 0.003 0.000 ARG B 817 *********************** 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 161 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 129 time to evaluate : 1.722 Fit side-chains revert: symmetry clash REVERT: A 594 ARG cc_start: 0.7872 (OUTLIER) cc_final: 0.7618 (mmp-170) REVERT: A 749 ARG cc_start: 0.7726 (mtp180) cc_final: 0.7479 (mmm-85) REVERT: B 376 ARG cc_start: 0.7055 (mmm160) cc_final: 0.6801 (mmm160) outliers start: 32 outliers final: 15 residues processed: 151 average time/residue: 1.1902 time to fit residues: 196.3822 Evaluate side-chains 143 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.186 ------------------------------------------------------------------------------- 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 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 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 594 ARG 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: 2.9990 chunk 79 optimal weight: 0.9990 chunk 101 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 77 optimal weight: 0.4980 chunk 138 optimal weight: 0.6980 chunk 86 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1013 ASN B 706 HIS B 937 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11632 Z= 0.179 Angle : 0.463 5.161 15774 Z= 0.252 Chirality : 0.040 0.167 1792 Planarity : 0.004 0.043 1945 Dihedral : 8.036 84.687 1640 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.06 % Allowed : 12.95 % Favored : 84.99 % 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: 1.84 (0.22), residues: 1420 helix: 2.62 (0.18), residues: 780 sheet: 0.34 (0.40), residues: 156 loop : -0.87 (0.27), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 779 HIS 0.005 0.001 HIS A 828 PHE 0.018 0.001 PHE B 911 TYR 0.010 0.001 TYR A 827 ARG 0.002 0.000 ARG A 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 155 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 131 time to evaluate : 1.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 749 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7455 (mmm-85) REVERT: B 376 ARG cc_start: 0.7028 (mmm160) cc_final: 0.6768 (mmm160) outliers start: 24 outliers final: 16 residues processed: 144 average time/residue: 1.1519 time to fit residues: 181.1421 Evaluate side-chains 143 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 384 ASN Chi-restraints excluded: chain A residue 602 ASP 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 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 446 THR 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 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: 2.9990 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 94 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 126 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.8012 moved from start: 0.2436 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= 0.403 Angle : 0.606 7.457 15774 Z= 0.322 Chirality : 0.047 0.174 1792 Planarity : 0.005 0.044 1945 Dihedral : 8.966 98.305 1640 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 2.49 % Allowed : 12.61 % 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: 1.36 (0.22), residues: 1420 helix: 2.13 (0.18), residues: 784 sheet: 0.25 (0.39), residues: 156 loop : -0.97 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 806 HIS 0.007 0.002 HIS A 828 PHE 0.021 0.002 PHE B 911 TYR 0.015 0.002 TYR A 254 ARG 0.004 0.001 ARG B 417 *********************** 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 162 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 1.432 Fit side-chains revert: symmetry clash REVERT: A 594 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7613 (mmp-170) REVERT: A 749 ARG cc_start: 0.7775 (mtp180) cc_final: 0.7495 (mmm-85) REVERT: A 1108 SER cc_start: 0.8302 (OUTLIER) cc_final: 0.7921 (m) REVERT: B 1108 SER cc_start: 0.8311 (OUTLIER) cc_final: 0.7910 (m) outliers start: 29 outliers final: 14 residues processed: 152 average time/residue: 1.1401 time to fit residues: 189.2673 Evaluate side-chains 147 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 594 ARG Chi-restraints excluded: chain A residue 602 ASP 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: 0.0370 chunk 121 optimal weight: 0.8980 chunk 129 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 101 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 116 optimal weight: 0.6980 chunk 122 optimal weight: 0.5980 chunk 128 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.6258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 937 HIS B 706 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 11632 Z= 0.160 Angle : 0.459 5.048 15774 Z= 0.250 Chirality : 0.040 0.166 1792 Planarity : 0.004 0.043 1945 Dihedral : 7.967 78.871 1640 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 1.89 % Allowed : 13.46 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.22), residues: 1420 helix: 2.55 (0.18), residues: 784 sheet: 0.38 (0.39), residues: 156 loop : -0.83 (0.27), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 779 HIS 0.004 0.001 HIS A 828 PHE 0.017 0.001 PHE B 911 TYR 0.011 0.001 TYR A 952 ARG 0.002 0.000 ARG B 817 *********************** 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 149 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 127 time to evaluate : 1.296 Fit side-chains revert: symmetry clash REVERT: A 749 ARG cc_start: 0.7702 (mtp180) cc_final: 0.7459 (mmm-85) REVERT: B 671 ILE cc_start: 0.7615 (OUTLIER) cc_final: 0.7372 (mm) outliers start: 22 outliers final: 12 residues processed: 138 average time/residue: 1.1843 time to fit residues: 178.1958 Evaluate side-chains 140 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.261 ------------------------------------------------------------------------------- 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 602 ASP Chi-restraints excluded: chain A residue 673 VAL 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 671 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 817 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 136 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 95 optimal weight: 0.5980 chunk 143 optimal weight: 3.9990 chunk 132 optimal weight: 0.0070 chunk 114 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- 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 B 706 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 11632 Z= 0.152 Angle : 0.450 5.127 15774 Z= 0.244 Chirality : 0.040 0.166 1792 Planarity : 0.004 0.044 1945 Dihedral : 7.499 75.545 1640 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 1.72 % Allowed : 13.46 % Favored : 84.82 % 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: 2.00 (0.22), residues: 1420 helix: 2.73 (0.18), residues: 776 sheet: 0.69 (0.39), residues: 152 loop : -0.85 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 779 HIS 0.003 0.001 HIS A 828 PHE 0.015 0.001 PHE B 911 TYR 0.010 0.001 TYR A 827 ARG 0.002 0.000 ARG A 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 147 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 127 time to evaluate : 1.290 Fit side-chains REVERT: A 749 ARG cc_start: 0.7669 (mtp180) cc_final: 0.7433 (mmm-85) REVERT: B 671 ILE cc_start: 0.7699 (OUTLIER) cc_final: 0.7456 (mm) outliers start: 20 outliers final: 13 residues processed: 137 average time/residue: 1.1896 time to fit residues: 177.6894 Evaluate side-chains 141 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 446 THR Chi-restraints excluded: chain A residue 602 ASP Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 1066 ASP 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 656 MET Chi-restraints excluded: chain B residue 671 ILE Chi-restraints excluded: chain B residue 673 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 0.0970 chunk 114 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 100 optimal weight: 0.6980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.139722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.110152 restraints weight = 12723.983| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 1.76 r_work: 0.3147 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2660 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= 0.165 Angle : 0.458 5.592 15774 Z= 0.248 Chirality : 0.040 0.160 1792 Planarity : 0.004 0.044 1945 Dihedral : 7.286 77.479 1636 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.46 % Allowed : 13.55 % Favored : 84.99 % 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: 2.01 (0.22), residues: 1420 helix: 2.65 (0.18), residues: 784 sheet: 0.70 (0.39), residues: 152 loop : -0.74 (0.27), residues: 484 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 0.015 0.001 PHE B 911 TYR 0.010 0.001 TYR A 827 ARG 0.002 0.000 ARG A 687 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3980.84 seconds wall clock time: 71 minutes 31.91 seconds (4291.91 seconds total)