Starting phenix.real_space_refine on Thu Mar 14 18:10:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/03_2024/8k3t_36859_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/03_2024/8k3t_36859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/03_2024/8k3t_36859.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/03_2024/8k3t_36859.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/03_2024/8k3t_36859_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3t_36859/03_2024/8k3t_36859_updated.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.052 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 4 5.21 5 S 58 5.16 5 C 6178 2.51 5 N 1482 2.21 5 O 1682 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 457": "OE1" <-> "OE2" Residue "A PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 526": "OD1" <-> "OD2" Residue "A PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 717": "OD1" <-> "OD2" Residue "A TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 758": "NH1" <-> "NH2" Residue "A ARG 759": "NH1" <-> "NH2" Residue "A TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 794": "OE1" <-> "OE2" Residue "A TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1060": "OE1" <-> "OE2" Residue "A TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 413": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 418": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 457": "OE1" <-> "OE2" Residue "B PHE 523": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 526": "OD1" <-> "OD2" Residue "B PHE 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 589": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 613": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 652": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 668": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 670": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 681": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 683": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 694": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 705": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 717": "OD1" <-> "OD2" Residue "B TYR 736": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 753": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 758": "NH1" <-> "NH2" Residue "B TYR 770": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 794": "OE1" <-> "OE2" Residue "B TYR 797": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 812": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 878": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 925": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 942": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 945": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 952": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 959": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1046": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1052": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1060": "OE1" <-> "OE2" Residue "B TYR 1097": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 1119": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 1125": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9410 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4630 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 283 Chain: "B" Number of atoms: 4630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 4630 Classifications: {'peptide': 627} Incomplete info: {'truncation_to_alanine': 122} Link IDs: {'PTRANS': 17, 'TRANS': 609} Chain breaks: 4 Unresolved non-hydrogen bonds: 496 Unresolved non-hydrogen angles: 603 Unresolved non-hydrogen dihedrals: 418 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 7, 'PHE:plan': 6, 'GLU:plan': 17, 'ARG:plan': 16} Unresolved non-hydrogen planarities: 283 Chain: "A" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 75 Unusual residues: {' MG': 2, 'POV': 1, 'UDP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 5.49, per 1000 atoms: 0.58 Number of scatterers: 9410 At special positions: 0 Unit cell: (113.42, 109.18, 100.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 58 16.00 P 6 15.00 Mg 4 11.99 O 1682 8.00 N 1482 7.00 C 6178 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.89 Conformation dependent library (CDL) restraints added in 1.5 seconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2396 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 50 helices and 6 sheets defined 61.1% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 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 439 No H-bonds generated for 'chain 'A' and resid 436 through 439' 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 removed outlier: 4.155A pdb=" N LEU A 512 " --> pdb=" O ARG A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 579 through 586 removed outlier: 3.617A pdb=" N ARG A 583 " --> pdb=" O ILE A 579 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 611 through 620 removed outlier: 3.817A pdb=" N GLU A 618 " --> pdb=" O GLN A 614 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE A 619 " --> pdb=" O LEU A 615 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG A 620 " --> pdb=" O TRP A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 643 removed outlier: 5.509A pdb=" N LYS A 641 " --> pdb=" O ARG A 638 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU A 643 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 668 removed outlier: 3.539A pdb=" N GLN A 650 " --> pdb=" O LEU A 646 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LYS A 662 " --> pdb=" O ASN A 658 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N THR A 663 " --> pdb=" O ILE A 659 " (cutoff:3.500A) removed outlier: 3.753A 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 725 removed outlier: 5.695A pdb=" N TYR A 713 " --> pdb=" O SER A 709 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU A 714 " --> pdb=" O SER A 710 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N ALA A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLU A 716 " --> pdb=" O MET A 712 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP A 717 " --> pdb=" O TYR A 713 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG A 718 " --> pdb=" O LEU A 714 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N CYS A 721 " --> pdb=" O ASP A 717 " (cutoff:3.500A) Processing helix chain 'A' and resid 750 through 780 removed outlier: 4.627A pdb=" N ARG A 759 " --> pdb=" O LEU A 755 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TRP A 760 " --> pdb=" O GLN A 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN A 762 " --> pdb=" O ARG A 758 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR A 776 " --> pdb=" O PHE A 772 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N ARG A 777 " --> pdb=" O CYS A 773 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL A 778 " --> pdb=" O HIS A 774 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N TRP A 779 " --> pdb=" O PHE A 775 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER A 780 " --> pdb=" O TYR A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 785 through 806 Processing helix chain 'A' and resid 808 through 827 Processing helix chain 'A' and resid 831 through 855 Processing helix chain 'A' and resid 859 through 892 removed outlier: 4.026A pdb=" N GLU A 862 " --> pdb=" O LYS A 859 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N LYS A 863 " --> pdb=" O SER A 860 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N PHE A 864 " --> pdb=" O THR A 861 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE A 884 " --> pdb=" O PHE A 881 " (cutoff:3.500A) Processing helix chain 'A' and resid 911 through 932 Processing helix chain 'A' and resid 943 through 954 Proline residue: A 950 - end of helix Processing helix chain 'A' and resid 956 through 963 Processing helix chain 'A' and resid 1028 through 1059 removed outlier: 4.176A pdb=" N ILE A1045 " --> pdb=" O SER A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1064 through 1073 Processing helix chain 'A' and resid 1092 through 1129 removed outlier: 3.574A pdb=" N LEU A1102 " --> pdb=" O PHE A1098 " (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 439 No H-bonds generated for 'chain 'B' and resid 436 through 439' 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 removed outlier: 4.154A pdb=" N LEU B 512 " --> pdb=" O ARG B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 579 through 586 removed outlier: 3.615A pdb=" N ARG B 583 " --> pdb=" O ILE B 579 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 593 Processing helix chain 'B' and resid 611 through 620 removed outlier: 3.818A pdb=" N GLU B 618 " --> pdb=" O GLN B 614 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE B 619 " --> pdb=" O LEU B 615 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ARG B 620 " --> pdb=" O TRP B 616 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 643 removed outlier: 5.508A pdb=" N LYS B 641 " --> pdb=" O ARG B 638 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N LEU B 643 " --> pdb=" O VAL B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 645 through 668 removed outlier: 3.540A pdb=" N GLN B 650 " --> pdb=" O LEU B 646 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LYS B 662 " --> pdb=" O ASN B 658 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N THR B 663 " --> pdb=" O ILE B 659 " (cutoff:3.500A) removed outlier: 3.753A 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 725 removed outlier: 5.695A pdb=" N TYR B 713 " --> pdb=" O SER B 709 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU B 714 " --> pdb=" O SER B 710 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N ALA B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N GLU B 716 " --> pdb=" O MET B 712 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ASP B 717 " --> pdb=" O TYR B 713 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ARG B 718 " --> pdb=" O LEU B 714 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU B 720 " --> pdb=" O GLU B 716 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N CYS B 721 " --> pdb=" O ASP B 717 " (cutoff:3.500A) Processing helix chain 'B' and resid 750 through 780 removed outlier: 4.626A pdb=" N ARG B 759 " --> pdb=" O LEU B 755 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TRP B 760 " --> pdb=" O GLN B 756 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN B 762 " --> pdb=" O ARG B 758 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N TYR B 776 " --> pdb=" O PHE B 772 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N ARG B 777 " --> pdb=" O CYS B 773 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N VAL B 778 " --> pdb=" O HIS B 774 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TRP B 779 " --> pdb=" O PHE B 775 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N SER B 780 " --> pdb=" O TYR B 776 " (cutoff:3.500A) Processing helix chain 'B' and resid 785 through 806 Processing helix chain 'B' and resid 808 through 827 Processing helix chain 'B' and resid 831 through 855 Processing helix chain 'B' and resid 859 through 892 removed outlier: 4.028A pdb=" N GLU B 862 " --> pdb=" O LYS B 859 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N LYS B 863 " --> pdb=" O SER B 860 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N PHE B 864 " --> pdb=" O THR B 861 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 884 " --> pdb=" O PHE B 881 " (cutoff:3.500A) Processing helix chain 'B' and resid 911 through 932 Processing helix chain 'B' and resid 943 through 954 Proline residue: B 950 - end of helix Processing helix chain 'B' and resid 956 through 963 Processing helix chain 'B' and resid 1028 through 1059 removed outlier: 4.176A pdb=" N ILE B1045 " --> pdb=" O SER B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1064 through 1073 Processing helix chain 'B' and resid 1092 through 1129 removed outlier: 3.575A pdb=" N LEU B1102 " --> pdb=" O PHE B1098 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 417 through 421 removed outlier: 3.683A pdb=" N HIS A 540 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N ILE A 493 " --> pdb=" O GLN A 566 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N LEU A 568 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL A 495 " --> pdb=" O LEU A 568 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS A 570 " --> pdb=" O VAL A 495 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ILE A 497 " --> pdb=" O CYS A 570 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 572 " --> pdb=" O ILE A 497 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N SER A 499 " --> pdb=" O LYS A 572 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU A 448 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS A 496 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N LEU A 450 " --> pdb=" O CYS A 496 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE A 498 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N VAL A 452 " --> pdb=" O ILE A 498 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE A 597 " --> pdb=" O MET A 449 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL A 451 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR A 599 " --> pdb=" O VAL A 451 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR A 453 " --> pdb=" O THR A 599 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU A 601 " --> pdb=" O THR A 453 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N GLY A 625 " --> pdb=" O ARG A 682 " (cutoff:3.500A) removed outlier: 7.121A pdb=" N ILE A 733 " --> pdb=" O GLY A 625 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA A 627 " --> pdb=" O ILE A 733 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LYS A 735 " --> pdb=" O ALA A 627 " (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: 6.771A pdb=" N SER A 555 " --> pdb=" O THR A 547 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 417 through 421 removed outlier: 3.682A pdb=" N HIS B 540 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N ILE B 493 " --> pdb=" O GLN B 566 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N LEU B 568 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N VAL B 495 " --> pdb=" O LEU B 568 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N CYS B 570 " --> pdb=" O VAL B 495 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ILE B 497 " --> pdb=" O CYS B 570 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS B 572 " --> pdb=" O ILE B 497 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N SER B 499 " --> pdb=" O LYS B 572 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU B 448 " --> pdb=" O VAL B 494 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N CYS B 496 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 450 " --> pdb=" O CYS B 496 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE B 498 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N VAL B 452 " --> pdb=" O ILE B 498 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE B 597 " --> pdb=" O MET B 449 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL B 451 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR B 599 " --> pdb=" O VAL B 451 " (cutoff:3.500A) removed outlier: 8.095A pdb=" N THR B 453 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU B 601 " --> pdb=" O THR B 453 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N GLY B 625 " --> pdb=" O ARG B 682 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N ILE B 733 " --> pdb=" O GLY B 625 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N ALA B 627 " --> pdb=" O ILE B 733 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS B 735 " --> pdb=" O ALA B 627 " (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: 6.771A pdb=" N SER B 555 " --> pdb=" O THR B 547 " (cutoff:3.500A) 554 hydrogen bonds defined for protein. 1458 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 4.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1629 1.32 - 1.45: 2673 1.45 - 1.57: 5244 1.57 - 1.69: 10 1.69 - 1.81: 86 Bond restraints: 9642 Sorted by residual: bond pdb=" O1A UDP B1502 " pdb=" PA UDP B1502 " ideal model delta sigma weight residual 1.482 1.527 -0.045 1.00e-02 1.00e+04 1.99e+01 bond pdb=" O1A UDP A1502 " pdb=" PA UDP A1502 " ideal model delta sigma weight residual 1.482 1.526 -0.044 1.00e-02 1.00e+04 1.92e+01 bond pdb=" N ILE A 493 " pdb=" CA ILE A 493 " ideal model delta sigma weight residual 1.457 1.493 -0.037 1.15e-02 7.56e+03 1.01e+01 bond pdb=" N VAL B 533 " pdb=" CA VAL B 533 " ideal model delta sigma weight residual 1.459 1.495 -0.035 1.15e-02 7.56e+03 9.53e+00 bond pdb=" N ILE B 493 " pdb=" CA ILE B 493 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.15e-02 7.56e+03 9.37e+00 ... (remaining 9637 not shown) Histogram of bond angle deviations from ideal: 97.39 - 104.77: 130 104.77 - 112.15: 4981 112.15 - 119.54: 3164 119.54 - 126.92: 4794 126.92 - 134.30: 103 Bond angle restraints: 13172 Sorted by residual: angle pdb=" CA PHE B 831 " pdb=" C PHE B 831 " pdb=" N ASN B 832 " ideal model delta sigma weight residual 118.27 108.41 9.86 1.59e+00 3.96e-01 3.84e+01 angle pdb=" CA PHE A 831 " pdb=" C PHE A 831 " pdb=" N ASN A 832 " ideal model delta sigma weight residual 118.27 108.42 9.85 1.59e+00 3.96e-01 3.84e+01 angle pdb=" O5' UDP A1502 " pdb=" PA UDP A1502 " pdb=" O1A UDP A1502 " ideal model delta sigma weight residual 106.70 111.20 -4.50 1.00e+00 1.00e+00 2.03e+01 angle pdb=" O5' UDP B1502 " pdb=" PA UDP B1502 " pdb=" O1A UDP B1502 " ideal model delta sigma weight residual 106.70 111.18 -4.48 1.00e+00 1.00e+00 2.01e+01 angle pdb=" O2A UDP B1502 " pdb=" PA UDP B1502 " pdb=" O3A UDP B1502 " ideal model delta sigma weight residual 105.97 110.25 -4.28 1.00e+00 1.00e+00 1.83e+01 ... (remaining 13167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.20: 5282 23.20 - 46.40: 230 46.40 - 69.59: 42 69.59 - 92.79: 24 92.79 - 115.99: 2 Dihedral angle restraints: 5580 sinusoidal: 1878 harmonic: 3702 Sorted by residual: dihedral pdb=" C27 POV B1503 " pdb=" C28 POV B1503 " pdb=" C29 POV B1503 " pdb="C210 POV B1503 " ideal model delta sinusoidal sigma weight residual 127.48 -116.53 -115.99 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" C27 POV A1503 " pdb=" C28 POV A1503 " pdb=" C29 POV A1503 " pdb="C210 POV A1503 " ideal model delta sinusoidal sigma weight residual 127.48 -116.59 -115.93 1 3.00e+01 1.11e-03 1.53e+01 dihedral pdb=" CA PHE A 911 " pdb=" C PHE A 911 " pdb=" N ARG A 912 " pdb=" CA ARG A 912 " ideal model delta harmonic sigma weight residual 180.00 161.62 18.38 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 5577 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 939 0.041 - 0.082: 444 0.082 - 0.124: 128 0.124 - 0.165: 29 0.165 - 0.206: 10 Chirality restraints: 1550 Sorted by residual: chirality pdb=" CA ILE B 719 " pdb=" N ILE B 719 " pdb=" C ILE B 719 " pdb=" CB ILE B 719 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE A 719 " pdb=" N ILE A 719 " pdb=" C ILE A 719 " pdb=" CB ILE A 719 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA VAL A 421 " pdb=" N VAL A 421 " pdb=" C VAL A 421 " pdb=" CB VAL A 421 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 1547 not shown) Planarity restraints: 1612 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV A1503 " -0.025 2.00e-02 2.50e+03 4.53e-02 2.06e+01 pdb=" C29 POV A1503 " 0.059 2.00e-02 2.50e+03 pdb="C210 POV A1503 " -0.059 2.00e-02 2.50e+03 pdb="C211 POV A1503 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1503 " 0.025 2.00e-02 2.50e+03 4.51e-02 2.04e+01 pdb=" C29 POV B1503 " -0.059 2.00e-02 2.50e+03 pdb="C210 POV B1503 " 0.059 2.00e-02 2.50e+03 pdb="C211 POV B1503 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 606 " 0.031 5.00e-02 4.00e+02 4.70e-02 3.54e+00 pdb=" N PRO A 607 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 607 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 607 " 0.026 5.00e-02 4.00e+02 ... (remaining 1609 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1978 2.76 - 3.30: 10127 3.30 - 3.83: 15917 3.83 - 4.36: 17765 4.36 - 4.90: 29973 Nonbonded interactions: 75760 Sorted by model distance: nonbonded pdb=" O ALA A 511 " pdb=" OG SER A 515 " model vdw 2.225 2.440 nonbonded pdb=" O ALA B 511 " pdb=" OG SER B 515 " model vdw 2.225 2.440 nonbonded pdb=" OE2 GLU A1060 " pdb=" OG1 THR A1091 " model vdw 2.262 2.440 nonbonded pdb=" OE2 GLU B1060 " pdb=" OG1 THR B1091 " model vdw 2.263 2.440 nonbonded pdb=" O1A UDP B1502 " pdb="MG MG B1504 " model vdw 2.287 2.170 ... (remaining 75755 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 2.800 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 27.620 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.081 9642 Z= 0.613 Angle : 0.929 10.229 13172 Z= 0.555 Chirality : 0.052 0.206 1550 Planarity : 0.005 0.047 1612 Dihedral : 15.004 115.988 3184 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.12 % Allowed : 1.34 % Favored : 97.54 % 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: 0.41 (0.25), residues: 1234 helix: 1.11 (0.20), residues: 672 sheet: -0.96 (0.44), residues: 154 loop : -0.47 (0.34), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 806 HIS 0.006 0.002 HIS B 783 PHE 0.021 0.002 PHE A1052 TYR 0.028 0.002 TYR B 878 ARG 0.004 0.001 ARG B 817 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 153 time to evaluate : 1.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 ASN cc_start: 0.3025 (OUTLIER) cc_final: 0.2570 (p0) REVERT: A 437 GLN cc_start: 0.8616 (mm-40) cc_final: 0.8097 (mm110) REVERT: A 560 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8429 (tp40) REVERT: A 568 LEU cc_start: 0.7665 (tt) cc_final: 0.7193 (mp) REVERT: A 823 ILE cc_start: 0.9063 (tt) cc_final: 0.8791 (tt) REVERT: A 886 MET cc_start: 0.8323 (mtt) cc_final: 0.7679 (tmm) REVERT: B 411 ASN cc_start: 0.3117 (OUTLIER) cc_final: 0.2657 (p0) REVERT: B 437 GLN cc_start: 0.8641 (mm-40) cc_final: 0.8137 (mm110) REVERT: B 560 GLN cc_start: 0.8779 (mm-40) cc_final: 0.8454 (tp40) REVERT: B 568 LEU cc_start: 0.7621 (tt) cc_final: 0.7191 (mp) REVERT: B 823 ILE cc_start: 0.9066 (tt) cc_final: 0.8786 (tt) REVERT: B 886 MET cc_start: 0.8316 (mtt) cc_final: 0.7693 (tmm) outliers start: 10 outliers final: 0 residues processed: 157 average time/residue: 0.1646 time to fit residues: 37.8455 Evaluate side-chains 111 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 109 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 ASN Chi-restraints excluded: chain B residue 411 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 0.6980 chunk 93 optimal weight: 2.9990 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN A 774 HIS B 411 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9642 Z= 0.208 Angle : 0.548 6.228 13172 Z= 0.300 Chirality : 0.041 0.177 1550 Planarity : 0.004 0.035 1612 Dihedral : 12.854 121.270 1474 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.12 % Allowed : 6.82 % Favored : 92.06 % 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: 0.97 (0.25), residues: 1234 helix: 1.48 (0.19), residues: 704 sheet: -0.56 (0.45), residues: 154 loop : -0.28 (0.34), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 806 HIS 0.005 0.001 HIS B 828 PHE 0.016 0.001 PHE A1052 TYR 0.016 0.002 TYR A 713 ARG 0.002 0.000 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 140 time to evaluate : 0.987 Fit side-chains REVERT: A 437 GLN cc_start: 0.8422 (mm-40) cc_final: 0.7861 (mm110) REVERT: A 560 GLN cc_start: 0.8732 (mm-40) cc_final: 0.8417 (tp40) REVERT: A 879 MET cc_start: 0.8653 (ttp) cc_final: 0.8327 (ttp) REVERT: A 938 MET cc_start: 0.8626 (tpp) cc_final: 0.8408 (tpp) REVERT: B 437 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8087 (mm110) REVERT: B 543 MET cc_start: 0.6813 (pmm) cc_final: 0.6427 (ptp) REVERT: B 560 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8472 (tp40) REVERT: B 568 LEU cc_start: 0.7619 (tt) cc_final: 0.7210 (mp) REVERT: B 879 MET cc_start: 0.8651 (ttp) cc_final: 0.8327 (ttp) REVERT: B 938 MET cc_start: 0.8635 (tpp) cc_final: 0.8397 (tpp) outliers start: 10 outliers final: 10 residues processed: 145 average time/residue: 0.1510 time to fit residues: 33.9564 Evaluate side-chains 119 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 20.0000 chunk 34 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 76 optimal weight: 8.9990 chunk 31 optimal weight: 6.9990 chunk 112 optimal weight: 0.0030 chunk 121 optimal weight: 4.9990 chunk 100 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 90 optimal weight: 0.4980 overall best weight: 1.2994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 774 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9642 Z= 0.189 Angle : 0.494 5.858 13172 Z= 0.267 Chirality : 0.040 0.197 1550 Planarity : 0.004 0.031 1612 Dihedral : 12.587 126.730 1470 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.68 % Allowed : 10.51 % Favored : 87.81 % 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: 1.18 (0.25), residues: 1234 helix: 1.62 (0.20), residues: 710 sheet: -0.33 (0.45), residues: 154 loop : -0.23 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 806 HIS 0.004 0.001 HIS A 828 PHE 0.026 0.001 PHE B 772 TYR 0.012 0.001 TYR A 713 ARG 0.002 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 111 time to evaluate : 1.129 Fit side-chains REVERT: A 560 GLN cc_start: 0.8701 (mm-40) cc_final: 0.8402 (tp40) REVERT: A 879 MET cc_start: 0.8735 (ttp) cc_final: 0.8495 (ttp) REVERT: A 938 MET cc_start: 0.8665 (tpp) cc_final: 0.8446 (tpp) REVERT: B 437 GLN cc_start: 0.8561 (mm-40) cc_final: 0.8046 (mm110) REVERT: B 560 GLN cc_start: 0.8723 (mm-40) cc_final: 0.8414 (tp40) REVERT: B 568 LEU cc_start: 0.7691 (tt) cc_final: 0.7242 (mp) REVERT: B 879 MET cc_start: 0.8731 (ttp) cc_final: 0.8493 (ttp) REVERT: B 938 MET cc_start: 0.8672 (tpp) cc_final: 0.8431 (tpp) outliers start: 15 outliers final: 12 residues processed: 119 average time/residue: 0.1562 time to fit residues: 29.3832 Evaluate side-chains 120 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 108 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 58 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 9642 Z= 0.352 Angle : 0.593 7.137 13172 Z= 0.318 Chirality : 0.042 0.200 1550 Planarity : 0.004 0.034 1612 Dihedral : 13.503 142.956 1470 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 3.13 % Allowed : 12.98 % Favored : 83.89 % 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: 0.90 (0.24), residues: 1234 helix: 1.27 (0.19), residues: 730 sheet: -0.32 (0.45), residues: 152 loop : -0.21 (0.34), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 806 HIS 0.004 0.001 HIS A 937 PHE 0.028 0.002 PHE A1052 TYR 0.015 0.002 TYR A 878 ARG 0.005 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.108 Fit side-chains revert: symmetry clash REVERT: A 476 MET cc_start: 0.8543 (mpp) cc_final: 0.7415 (mpp) REVERT: A 560 GLN cc_start: 0.8797 (mm-40) cc_final: 0.8496 (tp40) REVERT: A 1066 ASP cc_start: 0.8530 (OUTLIER) cc_final: 0.8306 (t70) REVERT: A 1070 MET cc_start: 0.8398 (tmm) cc_final: 0.8193 (tmm) REVERT: B 437 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8081 (mm110) REVERT: B 543 MET cc_start: 0.6780 (pmm) cc_final: 0.6439 (ptp) REVERT: B 560 GLN cc_start: 0.8742 (mm-40) cc_final: 0.8455 (tp40) REVERT: B 568 LEU cc_start: 0.7741 (tt) cc_final: 0.7244 (mp) REVERT: B 1066 ASP cc_start: 0.8525 (OUTLIER) cc_final: 0.8296 (t70) outliers start: 28 outliers final: 17 residues processed: 123 average time/residue: 0.1529 time to fit residues: 29.6020 Evaluate side-chains 127 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 717 ASP Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 0 optimal weight: 20.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 HIS ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 832 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9642 Z= 0.186 Angle : 0.491 7.389 13172 Z= 0.262 Chirality : 0.039 0.220 1550 Planarity : 0.003 0.032 1612 Dihedral : 13.155 143.175 1470 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.80 % Allowed : 14.65 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.25), residues: 1234 helix: 1.44 (0.19), residues: 744 sheet: -0.21 (0.46), residues: 152 loop : -0.42 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 806 HIS 0.004 0.001 HIS A 828 PHE 0.019 0.001 PHE A 772 TYR 0.011 0.001 TYR B 827 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7181 (tp-100) REVERT: A 476 MET cc_start: 0.8435 (mpp) cc_final: 0.8143 (mpp) REVERT: A 560 GLN cc_start: 0.8784 (mm-40) cc_final: 0.8472 (tp40) REVERT: A 606 MET cc_start: 0.5965 (mpp) cc_final: 0.5493 (mtt) REVERT: B 437 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8100 (mm110) REVERT: B 560 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8424 (tp40) REVERT: B 606 MET cc_start: 0.5974 (mpp) cc_final: 0.5525 (mtt) REVERT: B 1066 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8173 (t70) outliers start: 25 outliers final: 21 residues processed: 123 average time/residue: 0.1542 time to fit residues: 29.9873 Evaluate side-chains 135 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 113 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 40 optimal weight: 5.9990 chunk 107 optimal weight: 0.9980 chunk 23 optimal weight: 0.0020 chunk 70 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 chunk 99 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 62 optimal weight: 20.0000 overall best weight: 1.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 582 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9642 Z= 0.187 Angle : 0.492 7.046 13172 Z= 0.260 Chirality : 0.039 0.231 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.891 141.766 1470 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.13 % Allowed : 16.55 % Favored : 80.31 % 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: 1.08 (0.25), residues: 1234 helix: 1.51 (0.19), residues: 748 sheet: -0.22 (0.45), residues: 152 loop : -0.52 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 806 HIS 0.004 0.001 HIS A 828 PHE 0.022 0.001 PHE B 772 TYR 0.010 0.001 TYR B 713 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7768 (mm-40) cc_final: 0.7188 (tp-100) REVERT: A 606 MET cc_start: 0.5851 (mpp) cc_final: 0.5480 (mtt) REVERT: A 938 MET cc_start: 0.8490 (tpp) cc_final: 0.7479 (tpp) REVERT: A 1066 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8249 (t70) REVERT: B 437 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8115 (mm110) REVERT: B 519 TYR cc_start: 0.8337 (t80) cc_final: 0.7843 (t80) REVERT: B 560 GLN cc_start: 0.8751 (mm-40) cc_final: 0.8441 (tp40) REVERT: B 606 MET cc_start: 0.5866 (mpp) cc_final: 0.5508 (mtt) REVERT: B 938 MET cc_start: 0.8465 (tpp) cc_final: 0.7459 (tpp) REVERT: B 1066 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8243 (t70) outliers start: 28 outliers final: 23 residues processed: 126 average time/residue: 0.1506 time to fit residues: 29.9115 Evaluate side-chains 137 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 112 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 568 LEU Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1046 PHE Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 115 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 68 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 9.9990 chunk 119 optimal weight: 0.1980 chunk 74 optimal weight: 10.0000 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 756 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9642 Z= 0.268 Angle : 0.537 8.565 13172 Z= 0.284 Chirality : 0.040 0.233 1550 Planarity : 0.004 0.033 1612 Dihedral : 12.899 138.548 1470 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.13 % Allowed : 17.90 % Favored : 78.97 % 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: 0.98 (0.25), residues: 1234 helix: 1.42 (0.19), residues: 750 sheet: -0.30 (0.45), residues: 152 loop : -0.52 (0.34), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 806 HIS 0.003 0.001 HIS A 828 PHE 0.023 0.002 PHE B1052 TYR 0.009 0.001 TYR A 713 ARG 0.003 0.000 ARG A 436 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 111 time to evaluate : 1.054 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7772 (mm-40) cc_final: 0.7219 (tp-100) REVERT: A 876 MET cc_start: 0.9061 (tpp) cc_final: 0.8721 (tpp) REVERT: A 938 MET cc_start: 0.8584 (tpp) cc_final: 0.7612 (tpp) REVERT: A 1066 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8354 (t70) REVERT: B 437 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8371 (mm110) REVERT: B 476 MET cc_start: 0.8260 (mpp) cc_final: 0.7291 (mpp) REVERT: B 876 MET cc_start: 0.9057 (tpp) cc_final: 0.8718 (tpp) REVERT: B 938 MET cc_start: 0.8574 (tpp) cc_final: 0.7599 (tpp) REVERT: B 1066 ASP cc_start: 0.8558 (OUTLIER) cc_final: 0.8352 (t70) outliers start: 28 outliers final: 22 residues processed: 123 average time/residue: 0.1655 time to fit residues: 30.9019 Evaluate side-chains 135 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 526 ASP Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 673 VAL Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 526 ASP Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 20.0000 chunk 47 optimal weight: 0.2980 chunk 71 optimal weight: 30.0000 chunk 36 optimal weight: 30.0000 chunk 23 optimal weight: 0.0370 chunk 75 optimal weight: 20.0000 chunk 81 optimal weight: 0.0970 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 20.0000 chunk 93 optimal weight: 4.9990 chunk 108 optimal weight: 0.8980 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9642 Z= 0.134 Angle : 0.488 10.113 13172 Z= 0.250 Chirality : 0.039 0.239 1550 Planarity : 0.003 0.031 1612 Dihedral : 12.352 135.331 1470 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.80 % Allowed : 18.57 % Favored : 78.64 % 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: 1.22 (0.25), residues: 1234 helix: 1.71 (0.20), residues: 736 sheet: -0.17 (0.45), residues: 152 loop : -0.62 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 806 HIS 0.004 0.001 HIS B 828 PHE 0.017 0.001 PHE B 772 TYR 0.010 0.001 TYR A1067 ARG 0.002 0.000 ARG B 758 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 125 time to evaluate : 1.086 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7764 (mm-40) cc_final: 0.7230 (tp-100) REVERT: A 519 TYR cc_start: 0.8249 (t80) cc_final: 0.7735 (t80) REVERT: A 772 PHE cc_start: 0.8247 (t80) cc_final: 0.7971 (t80) REVERT: A 876 MET cc_start: 0.9059 (tpp) cc_final: 0.8725 (tpp) REVERT: A 925 TYR cc_start: 0.8126 (m-10) cc_final: 0.7839 (m-80) REVERT: A 938 MET cc_start: 0.8593 (tpp) cc_final: 0.7626 (tpp) REVERT: A 1052 PHE cc_start: 0.8501 (t80) cc_final: 0.8055 (t80) REVERT: A 1066 ASP cc_start: 0.8488 (OUTLIER) cc_final: 0.8288 (t70) REVERT: B 416 MET cc_start: 0.6838 (tmm) cc_final: 0.5024 (ttt) REVERT: B 437 GLN cc_start: 0.8736 (mm-40) cc_final: 0.8366 (mm110) REVERT: B 876 MET cc_start: 0.9075 (tpp) cc_final: 0.8740 (tpp) REVERT: B 925 TYR cc_start: 0.8107 (m-10) cc_final: 0.7819 (m-80) REVERT: B 938 MET cc_start: 0.8661 (tpp) cc_final: 0.7622 (tpp) REVERT: B 1052 PHE cc_start: 0.8504 (t80) cc_final: 0.8114 (t80) REVERT: B 1066 ASP cc_start: 0.8494 (OUTLIER) cc_final: 0.8274 (t70) outliers start: 25 outliers final: 20 residues processed: 132 average time/residue: 0.1617 time to fit residues: 33.1068 Evaluate side-chains 141 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 119 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1046 PHE Chi-restraints excluded: chain A residue 1066 ASP Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 653 GLU Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1066 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 67 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 100 optimal weight: 0.0050 chunk 105 optimal weight: 0.8980 chunk 110 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 overall best weight: 2.5800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.3144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9642 Z= 0.264 Angle : 0.528 7.654 13172 Z= 0.280 Chirality : 0.040 0.227 1550 Planarity : 0.003 0.032 1612 Dihedral : 12.246 130.582 1470 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.91 % Allowed : 19.35 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.25), residues: 1234 helix: 1.51 (0.19), residues: 750 sheet: -0.19 (0.45), residues: 152 loop : -0.52 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 806 HIS 0.002 0.001 HIS A 937 PHE 0.023 0.001 PHE B1052 TYR 0.009 0.001 TYR B 713 ARG 0.003 0.001 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.893 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7752 (mm-40) cc_final: 0.7220 (tp-100) REVERT: A 772 PHE cc_start: 0.8361 (t80) cc_final: 0.8093 (t80) REVERT: A 925 TYR cc_start: 0.8170 (m-10) cc_final: 0.7869 (m-80) REVERT: A 938 MET cc_start: 0.8632 (tpp) cc_final: 0.7629 (tpp) REVERT: B 437 GLN cc_start: 0.8764 (mm-40) cc_final: 0.8389 (mm110) REVERT: B 543 MET cc_start: 0.6741 (pmm) cc_final: 0.6515 (ptp) REVERT: B 876 MET cc_start: 0.9033 (tpp) cc_final: 0.8672 (tpp) REVERT: B 925 TYR cc_start: 0.8151 (m-10) cc_final: 0.7843 (m-80) REVERT: B 938 MET cc_start: 0.8571 (tpp) cc_final: 0.7528 (tpp) outliers start: 26 outliers final: 22 residues processed: 122 average time/residue: 0.1616 time to fit residues: 30.1938 Evaluate side-chains 137 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 115 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 459 HIS Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1070 MET Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 673 VAL Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1029 ASP Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 0.7980 chunk 71 optimal weight: 20.0000 chunk 55 optimal weight: 0.9980 chunk 81 optimal weight: 0.0870 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 30.0000 chunk 10 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 60 optimal weight: 0.6980 chunk 78 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9642 Z= 0.146 Angle : 0.485 8.209 13172 Z= 0.253 Chirality : 0.039 0.228 1550 Planarity : 0.003 0.032 1612 Dihedral : 11.664 126.735 1470 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.35 % Allowed : 19.80 % Favored : 77.85 % 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: 1.23 (0.25), residues: 1234 helix: 1.65 (0.20), residues: 748 sheet: -0.08 (0.45), residues: 152 loop : -0.54 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 806 HIS 0.003 0.001 HIS A 828 PHE 0.019 0.001 PHE B 772 TYR 0.009 0.001 TYR B 455 ARG 0.002 0.000 ARG A 436 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.109 Fit side-chains revert: symmetry clash REVERT: A 437 GLN cc_start: 0.7837 (mm-40) cc_final: 0.7288 (tp-100) REVERT: A 772 PHE cc_start: 0.8274 (t80) cc_final: 0.8048 (t80) REVERT: A 876 MET cc_start: 0.9063 (tpp) cc_final: 0.8723 (tpp) REVERT: A 925 TYR cc_start: 0.8130 (m-10) cc_final: 0.7841 (m-80) REVERT: A 938 MET cc_start: 0.8615 (tpp) cc_final: 0.7600 (tpp) REVERT: A 1052 PHE cc_start: 0.8609 (t80) cc_final: 0.8183 (t80) REVERT: B 437 GLN cc_start: 0.8844 (mm-40) cc_final: 0.8469 (mm110) REVERT: B 876 MET cc_start: 0.9021 (tpp) cc_final: 0.8674 (tpp) REVERT: B 925 TYR cc_start: 0.8138 (m-10) cc_final: 0.7853 (m-80) REVERT: B 938 MET cc_start: 0.8688 (tpp) cc_final: 0.7634 (tpp) REVERT: B 1052 PHE cc_start: 0.8609 (t80) cc_final: 0.8169 (t80) outliers start: 21 outliers final: 18 residues processed: 127 average time/residue: 0.1750 time to fit residues: 33.5416 Evaluate side-chains 135 residues out of total 1138 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 117 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 612 ILE Chi-restraints excluded: chain A residue 653 GLU Chi-restraints excluded: chain A residue 717 ASP Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain A residue 832 ASN Chi-restraints excluded: chain A residue 850 PHE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 1029 ASP Chi-restraints excluded: chain A residue 1040 ARG Chi-restraints excluded: chain A residue 1118 ILE Chi-restraints excluded: chain B residue 422 THR Chi-restraints excluded: chain B residue 459 HIS Chi-restraints excluded: chain B residue 612 ILE Chi-restraints excluded: chain B residue 804 ILE Chi-restraints excluded: chain B residue 850 PHE Chi-restraints excluded: chain B residue 852 LEU Chi-restraints excluded: chain B residue 1118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 98 optimal weight: 20.0000 chunk 41 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 6.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 545 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.123445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.090678 restraints weight = 20986.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.093715 restraints weight = 9889.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.095573 restraints weight = 6309.973| |-----------------------------------------------------------------------------| r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9642 Z= 0.225 Angle : 0.516 7.623 13172 Z= 0.270 Chirality : 0.039 0.220 1550 Planarity : 0.003 0.032 1612 Dihedral : 11.035 118.695 1470 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.35 % Allowed : 20.13 % Favored : 77.52 % 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: 1.20 (0.25), residues: 1234 helix: 1.60 (0.20), residues: 740 sheet: -0.08 (0.46), residues: 152 loop : -0.44 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 806 HIS 0.002 0.001 HIS A 937 PHE 0.022 0.001 PHE A1052 TYR 0.009 0.001 TYR A 713 ARG 0.003 0.000 ARG A 436 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1634.32 seconds wall clock time: 30 minutes 26.47 seconds (1826.47 seconds total)