Starting phenix.real_space_refine on Sun Jun 22 01:03:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7tl1_25983/06_2025/7tl1_25983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tl1_25983/06_2025/7tl1_25983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7tl1_25983/06_2025/7tl1_25983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tl1_25983/06_2025/7tl1_25983.map" model { file = "/net/cci-nas-00/data/ceres_data/7tl1_25983/06_2025/7tl1_25983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tl1_25983/06_2025/7tl1_25983.cif" } resolution = 3.5 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= -0.002 sd= 0.160 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: 4 Type Number sf(0) Gaussians S 111 5.16 5 C 16045 2.51 5 N 4121 2.21 5 O 4832 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.74s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 25109 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 8251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1053, 8251 Classifications: {'peptide': 1053} Link IDs: {'PTRANS': 51, 'TRANS': 1001} Chain breaks: 5 Chain: "B" Number of atoms: 8143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1040, 8143 Classifications: {'peptide': 1040} Link IDs: {'PTRANS': 49, 'TRANS': 990} Chain breaks: 6 Chain: "C" Number of atoms: 8189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1045, 8189 Classifications: {'peptide': 1045} Link IDs: {'PTRANS': 51, 'TRANS': 993} Chain breaks: 6 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 126 Unusual residues: {'NAG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 9 Time building chain proxies: 15.25, per 1000 atoms: 0.61 Number of scatterers: 25109 At special positions: 0 Unit cell: (129.6, 130.68, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 111 16.00 O 4832 8.00 N 4121 7.00 C 16045 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.04 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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 Links applied ALPHA1-3 " BMA M 3 " - " MAN M 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG G 1 " - " NAG G 2 " " NAG M 1 " - " NAG M 2 " " NAG M 2 " - " BMA M 3 " " NAG O 1 " - " NAG O 2 " NAG-ASN " NAG A1201 " - " ASN A 343 " " NAG A1202 " - " ASN A 122 " " NAG A1203 " - " ASN A1098 " " NAG A1204 " - " ASN A 282 " " NAG A1205 " - " ASN A 61 " " NAG A1206 " - " ASN A 165 " " NAG A1207 " - " ASN A 331 " " NAG A1208 " - " ASN A 657 " " NAG A1209 " - " ASN A1134 " " NAG B1201 " - " ASN B1134 " " NAG B1202 " - " ASN B1098 " " NAG B1203 " - " ASN B1074 " " NAG B1204 " - " ASN B 801 " " NAG B1205 " - " ASN B 717 " " NAG B1206 " - " ASN B 709 " " NAG B1207 " - " ASN B 616 " " NAG B1208 " - " ASN B 282 " " NAG C1201 " - " ASN C 331 " " NAG C1202 " - " ASN C 234 " " NAG C1203 " - " ASN C 61 " " NAG C1204 " - " ASN C 657 " " NAG C1205 " - " ASN C1074 " " NAG C1206 " - " ASN C 709 " " NAG C1207 " - " ASN C1134 " " NAG C1208 " - " ASN C1098 " " NAG C1209 " - " ASN C 616 " " NAG D 1 " - " ASN B 234 " " NAG E 1 " - " ASN C 717 " " NAG G 1 " - " ASN A 234 " " NAG M 1 " - " ASN A 717 " " NAG O 1 " - " ASN A 801 " Time building additional restraints: 6.44 Conformation dependent library (CDL) restraints added in 3.4 seconds 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5892 Finding SS restraints... Secondary structure from input PDB file: 73 helices and 48 sheets defined 26.7% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.90 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.689A pdb=" N TYR A 369 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.866A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 616 through 618 No H-bonds generated for 'chain 'A' and resid 616 through 618' Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 634 through 638 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 747 through 753 Processing helix chain 'A' and resid 754 through 757 removed outlier: 3.984A pdb=" N GLY A 757 " --> pdb=" O LEU A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 754 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.709A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 Processing helix chain 'A' and resid 837 through 842 Processing helix chain 'A' and resid 848 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 890 Processing helix chain 'A' and resid 897 through 909 removed outlier: 3.546A pdb=" N ILE A 909 " --> pdb=" O ARG A 905 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.110A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 Processing helix chain 'A' and resid 941 through 944 removed outlier: 4.024A pdb=" N ALA A 944 " --> pdb=" O THR A 941 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 941 through 944' Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.992A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ASN A 955 " --> pdb=" O VAL A 951 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.958A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU A 996 " --> pdb=" O GLN A 992 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.417A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.227A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.438A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 618 through 623 removed outlier: 4.082A pdb=" N VAL B 622 " --> pdb=" O THR B 618 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 757 removed outlier: 3.844A pdb=" N GLN B 755 " --> pdb=" O ASN B 751 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N TYR B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 783 removed outlier: 4.317A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 848 through 857 removed outlier: 3.835A pdb=" N ALA B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.619A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.357A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.703A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 removed outlier: 3.513A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 1032 Processing helix chain 'B' and resid 1140 through 1146 removed outlier: 3.944A pdb=" N GLU B1144 " --> pdb=" O PRO B1140 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 4.368A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 387 Processing helix chain 'C' and resid 405 through 410 removed outlier: 4.379A pdb=" N ARG C 408 " --> pdb=" O ASP C 405 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.805A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 618 through 623 removed outlier: 4.113A pdb=" N VAL C 622 " --> pdb=" O THR C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 755 removed outlier: 4.005A pdb=" N GLN C 755 " --> pdb=" O ASN C 751 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.727A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 826 Processing helix chain 'C' and resid 837 through 842 Processing helix chain 'C' and resid 851 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 removed outlier: 3.776A pdb=" N ALA C 890 " --> pdb=" O TRP C 886 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 909 removed outlier: 3.741A pdb=" N ILE C 909 " --> pdb=" O ARG C 905 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1140 through 1147 removed outlier: 4.130A pdb=" N GLU C1144 " --> pdb=" O PRO C1140 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 7.352A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N HIS A 207 " --> pdb=" O LEU A 223 " (cutoff:3.500A) removed outlier: 9.249A pdb=" N LEU A 223 " --> pdb=" O HIS A 207 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 43 removed outlier: 3.511A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) removed outlier: 5.811A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 4.064A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 4.032A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 5.255A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 314 Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 319 Processing sheet with id=AA7, first strand: chain 'A' and resid 325 through 328 removed outlier: 5.550A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.627A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 453 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.195A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 702 through 704 Processing sheet with id=AB5, first strand: chain 'A' and resid 712 through 715 removed outlier: 3.928A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 6.660A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 718 through 728 Processing sheet with id=AB8, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.623A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AC1, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 30 removed outlier: 8.385A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N HIS B 207 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N LEU B 223 " --> pdb=" O HIS B 207 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 4.060A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 84 through 85 removed outlier: 4.150A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 311 through 319 removed outlier: 6.988A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY B 594 " --> pdb=" O GLN B 613 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 325 through 328 removed outlier: 5.603A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.581A pdb=" N TYR B 396 " --> pdb=" O SER B 514 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AC9, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD1, first strand: chain 'B' and resid 473 through 474 removed outlier: 3.635A pdb=" N TYR B 473 " --> pdb=" O TYR B 489 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TYR B 489 " --> pdb=" O TYR B 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'B' and resid 654 through 655 removed outlier: 5.799A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.477A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 702 through 704 Processing sheet with id=AD4, first strand: chain 'B' and resid 711 through 713 removed outlier: 3.625A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL B1104 " --> pdb=" O GLN B1113 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.514A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 717 through 728 removed outlier: 6.514A pdb=" N ASN B 717 " --> pdb=" O ALA B1070 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 734 through 736 Processing sheet with id=AD8, first strand: chain 'B' and resid 1081 through 1082 Processing sheet with id=AD9, first strand: chain 'B' and resid 1089 through 1090 Processing sheet with id=AE1, first strand: chain 'C' and resid 28 through 30 removed outlier: 7.853A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.711A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 9.149A pdb=" N HIS C 207 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 9.181A pdb=" N LEU C 223 " --> pdb=" O HIS C 207 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 4.060A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 84 through 85 removed outlier: 4.243A pdb=" N GLY C 103 " --> pdb=" O LEU C 241 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 311 through 319 removed outlier: 4.625A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 355 through 358 removed outlier: 3.625A pdb=" N ALA C 435 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR C 376 " --> pdb=" O ALA C 435 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.307A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 453 through 454 Processing sheet with id=AE8, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.136A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.544A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 713 Processing sheet with id=AF1, first strand: chain 'C' and resid 718 through 728 removed outlier: 3.507A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N MET C1050 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AF3, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.343A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 1062 hydrogen bonds defined for protein. 2892 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: 12.19 Time building geometry restraints manager: 7.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7915 1.34 - 1.46: 6193 1.46 - 1.58: 11433 1.58 - 1.71: 0 1.71 - 1.83: 135 Bond restraints: 25676 Sorted by residual: bond pdb=" C ALA B 372 " pdb=" N PRO B 373 " ideal model delta sigma weight residual 1.336 1.384 -0.048 1.20e-02 6.94e+03 1.63e+01 bond pdb=" C1 NAG A1203 " pdb=" O5 NAG A1203 " ideal model delta sigma weight residual 1.406 1.477 -0.071 2.00e-02 2.50e+03 1.25e+01 bond pdb=" N VAL B 367 " pdb=" CA VAL B 367 " ideal model delta sigma weight residual 1.461 1.493 -0.031 1.17e-02 7.31e+03 7.21e+00 bond pdb=" C1 NAG C1202 " pdb=" O5 NAG C1202 " ideal model delta sigma weight residual 1.406 1.459 -0.053 2.00e-02 2.50e+03 7.14e+00 bond pdb=" C1 NAG O 2 " pdb=" O5 NAG O 2 " ideal model delta sigma weight residual 1.406 1.454 -0.048 2.00e-02 2.50e+03 5.81e+00 ... (remaining 25671 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 34113 2.02 - 4.05: 717 4.05 - 6.07: 66 6.07 - 8.10: 25 8.10 - 10.12: 4 Bond angle restraints: 34925 Sorted by residual: angle pdb=" C ASN A 87 " pdb=" CA ASN A 87 " pdb=" CB ASN A 87 " ideal model delta sigma weight residual 116.54 110.79 5.75 1.15e+00 7.56e-01 2.50e+01 angle pdb=" CB GLU A1017 " pdb=" CG GLU A1017 " pdb=" CD GLU A1017 " ideal model delta sigma weight residual 112.60 120.23 -7.63 1.70e+00 3.46e-01 2.02e+01 angle pdb=" C ILE A 410 " pdb=" N ALA A 411 " pdb=" CA ALA A 411 " ideal model delta sigma weight residual 121.80 130.81 -9.01 2.44e+00 1.68e-01 1.36e+01 angle pdb=" C ASN A 122 " pdb=" N ALA A 123 " pdb=" CA ALA A 123 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.20e+01 angle pdb=" CA GLU A1017 " pdb=" CB GLU A1017 " pdb=" CG GLU A1017 " ideal model delta sigma weight residual 114.10 120.88 -6.78 2.00e+00 2.50e-01 1.15e+01 ... (remaining 34920 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.16: 15054 21.16 - 42.32: 651 42.32 - 63.48: 72 63.48 - 84.64: 23 84.64 - 105.80: 5 Dihedral angle restraints: 15805 sinusoidal: 6654 harmonic: 9151 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual -86.00 -166.07 80.07 1 1.00e+01 1.00e-02 7.94e+01 dihedral pdb=" CB CYS A1082 " pdb=" SG CYS A1082 " pdb=" SG CYS A1126 " pdb=" CB CYS A1126 " ideal model delta sinusoidal sigma weight residual -86.00 -158.34 72.34 1 1.00e+01 1.00e-02 6.69e+01 dihedral pdb=" CB CYS C1082 " pdb=" SG CYS C1082 " pdb=" SG CYS C1126 " pdb=" CB CYS C1126 " ideal model delta sinusoidal sigma weight residual -86.00 -157.80 71.80 1 1.00e+01 1.00e-02 6.60e+01 ... (remaining 15802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 3909 0.113 - 0.226: 164 0.226 - 0.339: 8 0.339 - 0.452: 0 0.452 - 0.565: 2 Chirality restraints: 4083 Sorted by residual: chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.27 -0.13 2.00e-02 2.50e+03 4.21e+01 chirality pdb=" C1 NAG C1207 " pdb=" ND2 ASN C1134 " pdb=" C2 NAG C1207 " pdb=" O5 NAG C1207 " both_signs ideal model delta sigma weight residual False -2.40 -1.83 -0.57 2.00e-01 2.50e+01 7.99e+00 chirality pdb=" C1 NAG A1203 " pdb=" ND2 ASN A1098 " pdb=" C2 NAG A1203 " pdb=" O5 NAG A1203 " both_signs ideal model delta sigma weight residual False -2.40 -2.91 0.51 2.00e-01 2.50e+01 6.39e+00 ... (remaining 4080 not shown) Planarity restraints: 4485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 1 " -0.263 2.00e-02 2.50e+03 2.24e-01 6.27e+02 pdb=" C7 NAG E 1 " 0.067 2.00e-02 2.50e+03 pdb=" C8 NAG E 1 " -0.169 2.00e-02 2.50e+03 pdb=" N2 NAG E 1 " 0.385 2.00e-02 2.50e+03 pdb=" O7 NAG E 1 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG E 2 " -0.071 2.00e-02 2.50e+03 5.82e-02 4.23e+01 pdb=" C7 NAG E 2 " 0.017 2.00e-02 2.50e+03 pdb=" C8 NAG E 2 " -0.053 2.00e-02 2.50e+03 pdb=" N2 NAG E 2 " 0.092 2.00e-02 2.50e+03 pdb=" O7 NAG E 2 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A1098 " 0.049 2.00e-02 2.50e+03 4.68e-02 2.73e+01 pdb=" CG ASN A1098 " -0.054 2.00e-02 2.50e+03 pdb=" OD1 ASN A1098 " 0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A1098 " -0.055 2.00e-02 2.50e+03 pdb=" C1 NAG A1203 " 0.050 2.00e-02 2.50e+03 ... (remaining 4482 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 7261 2.82 - 3.34: 20731 3.34 - 3.86: 40869 3.86 - 4.38: 46200 4.38 - 4.90: 82727 Nonbonded interactions: 197788 Sorted by model distance: nonbonded pdb=" OE1 GLU A 819 " pdb=" OG SER A1055 " model vdw 2.302 3.040 nonbonded pdb=" OH TYR A 756 " pdb=" OD1 ASP A 994 " model vdw 2.307 3.040 nonbonded pdb=" OE1 GLU C 819 " pdb=" OG SER C1055 " model vdw 2.311 3.040 nonbonded pdb=" OE1 GLU B 819 " pdb=" OG SER B1055 " model vdw 2.315 3.040 nonbonded pdb=" O ASN B 439 " pdb=" OG SER B 443 " model vdw 2.316 3.040 ... (remaining 197783 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 210 or resid 219 through 678 or resid 689 throu \ gh 844 or resid 850 through 1147 or resid 1201 through 1208)) selection = (chain 'B' and (resid 27 through 844 or resid 850 through 1147 or resid 1201 thr \ ough 1208)) selection = (chain 'C' and (resid 27 through 210 or resid 219 through 1147 or resid 1201 thr \ ough 1208)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'O' } 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: 1.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.930 Check model and map are aligned: 0.190 Set scattering table: 0.250 Process input model: 61.400 Find NCS groups from input model: 1.850 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 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 : 0.004 0.071 25756 Z= 0.208 Angle : 0.727 16.082 35123 Z= 0.386 Chirality : 0.054 0.565 4083 Planarity : 0.007 0.224 4454 Dihedral : 11.661 105.799 9787 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % 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: -0.64 (0.14), residues: 3098 helix: 0.04 (0.17), residues: 728 sheet: 0.42 (0.20), residues: 633 loop : -0.93 (0.14), residues: 1737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 633 HIS 0.022 0.001 HIS B 954 PHE 0.025 0.002 PHE B 833 TYR 0.033 0.002 TYR B 837 ARG 0.005 0.000 ARG A 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00575 ( 31) link_NAG-ASN : angle 4.01857 ( 93) link_BETA1-4 : bond 0.01059 ( 6) link_BETA1-4 : angle 3.74879 ( 18) link_ALPHA1-3 : bond 0.00494 ( 1) link_ALPHA1-3 : angle 1.25093 ( 3) hydrogen bonds : bond 0.07585 ( 1041) hydrogen bonds : angle 5.71619 ( 2892) SS BOND : bond 0.00228 ( 42) SS BOND : angle 1.12476 ( 84) covalent geometry : bond 0.00398 (25676) covalent geometry : angle 0.69175 (34925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 2.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 981 PHE cc_start: 0.6876 (m-10) cc_final: 0.6633 (m-10) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.3710 time to fit residues: 47.0030 Evaluate side-chains 62 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 2.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 264 optimal weight: 5.9990 chunk 237 optimal weight: 9.9990 chunk 131 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 160 optimal weight: 9.9990 chunk 126 optimal weight: 5.9990 chunk 245 optimal weight: 7.9990 chunk 94 optimal weight: 4.9990 chunk 149 optimal weight: 9.9990 chunk 182 optimal weight: 0.9980 chunk 284 optimal weight: 4.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 625 HIS A1106 GLN C 613 GLN C 751 ASN C 755 GLN C1106 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.056523 restraints weight = 80447.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.058301 restraints weight = 47282.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.058719 restraints weight = 32012.385| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 25756 Z= 0.237 Angle : 0.593 11.637 35123 Z= 0.304 Chirality : 0.047 0.475 4083 Planarity : 0.004 0.050 4454 Dihedral : 6.848 65.524 4159 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.26 % Allowed : 3.47 % Favored : 96.27 % 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: -0.18 (0.15), residues: 3098 helix: 1.23 (0.19), residues: 712 sheet: 0.21 (0.19), residues: 662 loop : -0.83 (0.14), residues: 1724 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 353 HIS 0.009 0.001 HIS B 954 PHE 0.027 0.002 PHE A 906 TYR 0.024 0.002 TYR B1067 ARG 0.008 0.001 ARG A 634 Details of bonding type rmsd link_NAG-ASN : bond 0.00512 ( 31) link_NAG-ASN : angle 2.79887 ( 93) link_BETA1-4 : bond 0.00890 ( 6) link_BETA1-4 : angle 2.70683 ( 18) link_ALPHA1-3 : bond 0.00502 ( 1) link_ALPHA1-3 : angle 2.73844 ( 3) hydrogen bonds : bond 0.04977 ( 1041) hydrogen bonds : angle 5.14489 ( 2892) SS BOND : bond 0.00364 ( 42) SS BOND : angle 0.85275 ( 84) covalent geometry : bond 0.00563 (25676) covalent geometry : angle 0.57163 (34925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 2.757 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.5051 (p90) cc_final: 0.4796 (p90) outliers start: 7 outliers final: 2 residues processed: 64 average time/residue: 0.3891 time to fit residues: 42.3635 Evaluate side-chains 55 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 3.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain B residue 633 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 188 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 166 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 221 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 254 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.086348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.056858 restraints weight = 79832.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058678 restraints weight = 44530.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059858 restraints weight = 31173.371| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.1121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 25756 Z= 0.135 Angle : 0.503 11.283 35123 Z= 0.257 Chirality : 0.045 0.430 4083 Planarity : 0.003 0.046 4454 Dihedral : 6.182 57.929 4159 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.33 % Allowed : 5.33 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3098 helix: 1.77 (0.20), residues: 713 sheet: 0.22 (0.19), residues: 657 loop : -0.69 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 886 HIS 0.008 0.001 HIS B 954 PHE 0.015 0.001 PHE B 833 TYR 0.023 0.001 TYR B1067 ARG 0.003 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00422 ( 31) link_NAG-ASN : angle 2.47849 ( 93) link_BETA1-4 : bond 0.00853 ( 6) link_BETA1-4 : angle 2.28197 ( 18) link_ALPHA1-3 : bond 0.01096 ( 1) link_ALPHA1-3 : angle 1.82105 ( 3) hydrogen bonds : bond 0.04195 ( 1041) hydrogen bonds : angle 4.90896 ( 2892) SS BOND : bond 0.00234 ( 42) SS BOND : angle 0.61466 ( 84) covalent geometry : bond 0.00313 (25676) covalent geometry : angle 0.48360 (34925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 4.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.5021 (p90) cc_final: 0.4675 (p90) outliers start: 9 outliers final: 5 residues processed: 60 average time/residue: 0.5405 time to fit residues: 56.9290 Evaluate side-chains 57 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 3.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 125 optimal weight: 2.9990 chunk 89 optimal weight: 0.0470 chunk 287 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 309 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 161 optimal weight: 0.6980 chunk 150 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 overall best weight: 1.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.087030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.057958 restraints weight = 80157.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.059845 restraints weight = 47428.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.060362 restraints weight = 30975.854| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25756 Z= 0.096 Angle : 0.466 10.815 35123 Z= 0.238 Chirality : 0.044 0.415 4083 Planarity : 0.003 0.044 4454 Dihedral : 5.573 58.694 4159 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.44 % Allowed : 6.14 % Favored : 93.43 % 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: 0.33 (0.15), residues: 3098 helix: 2.11 (0.20), residues: 714 sheet: 0.27 (0.19), residues: 666 loop : -0.62 (0.15), residues: 1718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 886 HIS 0.006 0.001 HIS B 954 PHE 0.013 0.001 PHE B 833 TYR 0.019 0.001 TYR B1067 ARG 0.002 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00407 ( 31) link_NAG-ASN : angle 2.33171 ( 93) link_BETA1-4 : bond 0.00802 ( 6) link_BETA1-4 : angle 2.22546 ( 18) link_ALPHA1-3 : bond 0.01074 ( 1) link_ALPHA1-3 : angle 1.98692 ( 3) hydrogen bonds : bond 0.03668 ( 1041) hydrogen bonds : angle 4.69216 ( 2892) SS BOND : bond 0.00178 ( 42) SS BOND : angle 0.53919 ( 84) covalent geometry : bond 0.00213 (25676) covalent geometry : angle 0.44803 (34925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 3.129 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.4933 (p90) cc_final: 0.4420 (p90) outliers start: 12 outliers final: 8 residues processed: 66 average time/residue: 0.5496 time to fit residues: 65.1153 Evaluate side-chains 61 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 4.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 582 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 353 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 290 optimal weight: 5.9990 chunk 298 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 187 optimal weight: 0.8980 chunk 145 optimal weight: 20.0000 chunk 208 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 132 optimal weight: 40.0000 chunk 142 optimal weight: 50.0000 chunk 36 optimal weight: 30.0000 chunk 210 optimal weight: 9.9990 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.086268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.057104 restraints weight = 80122.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059052 restraints weight = 46767.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.059773 restraints weight = 30373.739| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 25756 Z= 0.138 Angle : 0.491 10.527 35123 Z= 0.249 Chirality : 0.044 0.421 4083 Planarity : 0.003 0.044 4454 Dihedral : 5.403 57.494 4159 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 0.40 % Allowed : 6.98 % Favored : 92.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.15), residues: 3098 helix: 2.14 (0.20), residues: 720 sheet: 0.21 (0.19), residues: 673 loop : -0.63 (0.15), residues: 1705 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.006 0.001 HIS B 954 PHE 0.015 0.001 PHE B 833 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00392 ( 31) link_NAG-ASN : angle 2.34083 ( 93) link_BETA1-4 : bond 0.00768 ( 6) link_BETA1-4 : angle 2.24544 ( 18) link_ALPHA1-3 : bond 0.00962 ( 1) link_ALPHA1-3 : angle 1.74679 ( 3) hydrogen bonds : bond 0.04053 ( 1041) hydrogen bonds : angle 4.74148 ( 2892) SS BOND : bond 0.00227 ( 42) SS BOND : angle 0.56616 ( 84) covalent geometry : bond 0.00324 (25676) covalent geometry : angle 0.47335 (34925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 4.910 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.4995 (p90) cc_final: 0.4495 (p90) REVERT: B 1141 LEU cc_start: 0.8815 (tp) cc_final: 0.8600 (tt) outliers start: 11 outliers final: 8 residues processed: 65 average time/residue: 0.6137 time to fit residues: 74.5303 Evaluate side-chains 60 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 5.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 87 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 304 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 281 optimal weight: 2.9990 chunk 38 optimal weight: 30.0000 chunk 232 optimal weight: 5.9990 chunk 303 optimal weight: 0.9980 chunk 279 optimal weight: 0.9990 chunk 33 optimal weight: 5.9990 chunk 271 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN B1135 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.086172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.057036 restraints weight = 80682.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059183 restraints weight = 47524.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.059402 restraints weight = 31095.062| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25756 Z= 0.145 Angle : 0.494 10.537 35123 Z= 0.252 Chirality : 0.044 0.415 4083 Planarity : 0.003 0.043 4454 Dihedral : 5.282 54.197 4159 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.44 % Allowed : 7.67 % Favored : 91.89 % 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: 0.33 (0.15), residues: 3098 helix: 2.21 (0.20), residues: 720 sheet: 0.16 (0.19), residues: 680 loop : -0.63 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.006 0.001 HIS B 954 PHE 0.014 0.001 PHE B 833 TYR 0.021 0.001 TYR B1067 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00388 ( 31) link_NAG-ASN : angle 2.32157 ( 93) link_BETA1-4 : bond 0.00760 ( 6) link_BETA1-4 : angle 2.23592 ( 18) link_ALPHA1-3 : bond 0.00811 ( 1) link_ALPHA1-3 : angle 1.53699 ( 3) hydrogen bonds : bond 0.04112 ( 1041) hydrogen bonds : angle 4.75813 ( 2892) SS BOND : bond 0.00238 ( 42) SS BOND : angle 0.55750 ( 84) covalent geometry : bond 0.00343 (25676) covalent geometry : angle 0.47662 (34925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 3.078 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.5167 (p90) cc_final: 0.4720 (p90) REVERT: B 1141 LEU cc_start: 0.8849 (tp) cc_final: 0.8634 (tt) REVERT: C 731 MET cc_start: 0.9216 (ptt) cc_final: 0.8900 (ptt) outliers start: 12 outliers final: 10 residues processed: 64 average time/residue: 0.4837 time to fit residues: 57.7105 Evaluate side-chains 64 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 189 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 116 optimal weight: 30.0000 chunk 117 optimal weight: 10.0000 chunk 232 optimal weight: 4.9990 chunk 103 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 196 optimal weight: 0.9990 chunk 169 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.086897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057785 restraints weight = 79919.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059684 restraints weight = 47282.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.060306 restraints weight = 30856.311| |-----------------------------------------------------------------------------| r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 25756 Z= 0.092 Angle : 0.462 10.292 35123 Z= 0.235 Chirality : 0.044 0.398 4083 Planarity : 0.003 0.043 4454 Dihedral : 5.090 54.633 4159 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.40 % Allowed : 7.78 % Favored : 91.82 % 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: 0.48 (0.15), residues: 3098 helix: 2.42 (0.20), residues: 714 sheet: 0.27 (0.19), residues: 665 loop : -0.56 (0.15), residues: 1719 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 64 HIS 0.004 0.001 HIS B 954 PHE 0.017 0.001 PHE B 168 TYR 0.019 0.001 TYR B1067 ARG 0.002 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00402 ( 31) link_NAG-ASN : angle 2.22990 ( 93) link_BETA1-4 : bond 0.00792 ( 6) link_BETA1-4 : angle 2.17874 ( 18) link_ALPHA1-3 : bond 0.00877 ( 1) link_ALPHA1-3 : angle 1.45574 ( 3) hydrogen bonds : bond 0.03610 ( 1041) hydrogen bonds : angle 4.61790 ( 2892) SS BOND : bond 0.00167 ( 42) SS BOND : angle 0.46495 ( 84) covalent geometry : bond 0.00200 (25676) covalent geometry : angle 0.44482 (34925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 2.892 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7914 (t80) cc_final: 0.7593 (t80) REVERT: B 456 PHE cc_start: 0.5183 (p90) cc_final: 0.4767 (p90) REVERT: B 1141 LEU cc_start: 0.8809 (tp) cc_final: 0.8595 (tt) REVERT: C 428 ASP cc_start: 0.8639 (m-30) cc_final: 0.8398 (t70) outliers start: 11 outliers final: 9 residues processed: 66 average time/residue: 0.4383 time to fit residues: 49.6360 Evaluate side-chains 65 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 3.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 353 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 143 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 227 optimal weight: 9.9990 chunk 288 optimal weight: 0.0870 chunk 19 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 242 optimal weight: 7.9990 chunk 104 optimal weight: 5.9990 chunk 121 optimal weight: 10.0000 chunk 138 optimal weight: 20.0000 chunk 235 optimal weight: 10.0000 overall best weight: 3.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.085086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055815 restraints weight = 80139.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.057786 restraints weight = 46729.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.058532 restraints weight = 30033.186| |-----------------------------------------------------------------------------| r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 25756 Z= 0.208 Angle : 0.547 10.733 35123 Z= 0.279 Chirality : 0.046 0.432 4083 Planarity : 0.003 0.043 4454 Dihedral : 5.236 55.007 4159 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.51 % Allowed : 8.11 % Favored : 91.38 % 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: 0.28 (0.15), residues: 3098 helix: 2.19 (0.20), residues: 714 sheet: 0.12 (0.19), residues: 670 loop : -0.66 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 353 HIS 0.006 0.001 HIS B 954 PHE 0.016 0.001 PHE B 833 TYR 0.023 0.001 TYR B1067 ARG 0.004 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00415 ( 31) link_NAG-ASN : angle 2.39147 ( 93) link_BETA1-4 : bond 0.00731 ( 6) link_BETA1-4 : angle 2.34675 ( 18) link_ALPHA1-3 : bond 0.00786 ( 1) link_ALPHA1-3 : angle 1.59364 ( 3) hydrogen bonds : bond 0.04662 ( 1041) hydrogen bonds : angle 4.89509 ( 2892) SS BOND : bond 0.00339 ( 42) SS BOND : angle 0.66166 ( 84) covalent geometry : bond 0.00498 (25676) covalent geometry : angle 0.53083 (34925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 2.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.5370 (p90) cc_final: 0.4983 (p90) REVERT: B 1141 LEU cc_start: 0.8850 (tp) cc_final: 0.8640 (tt) outliers start: 14 outliers final: 9 residues processed: 66 average time/residue: 0.3471 time to fit residues: 40.7189 Evaluate side-chains 63 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 2.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 131 optimal weight: 6.9990 chunk 199 optimal weight: 0.8980 chunk 219 optimal weight: 0.0870 chunk 21 optimal weight: 4.9990 chunk 99 optimal weight: 7.9990 chunk 49 optimal weight: 8.9990 chunk 154 optimal weight: 7.9990 chunk 206 optimal weight: 9.9990 chunk 286 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.085631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056473 restraints weight = 80363.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.058110 restraints weight = 48649.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059108 restraints weight = 32746.566| |-----------------------------------------------------------------------------| r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 25756 Z= 0.156 Angle : 0.509 10.643 35123 Z= 0.259 Chirality : 0.045 0.417 4083 Planarity : 0.003 0.043 4454 Dihedral : 5.174 54.360 4159 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.40 % Allowed : 8.40 % Favored : 91.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.15), residues: 3098 helix: 2.28 (0.20), residues: 713 sheet: 0.13 (0.19), residues: 671 loop : -0.66 (0.15), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 886 HIS 0.005 0.001 HIS B 954 PHE 0.014 0.001 PHE B 833 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00380 ( 31) link_NAG-ASN : angle 2.32407 ( 93) link_BETA1-4 : bond 0.00766 ( 6) link_BETA1-4 : angle 2.28795 ( 18) link_ALPHA1-3 : bond 0.00662 ( 1) link_ALPHA1-3 : angle 1.39614 ( 3) hydrogen bonds : bond 0.04260 ( 1041) hydrogen bonds : angle 4.82438 ( 2892) SS BOND : bond 0.00251 ( 42) SS BOND : angle 0.55880 ( 84) covalent geometry : bond 0.00369 (25676) covalent geometry : angle 0.49277 (34925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 55 time to evaluate : 2.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.5347 (p90) cc_final: 0.4943 (p90) REVERT: B 1141 LEU cc_start: 0.8894 (tp) cc_final: 0.8676 (tt) outliers start: 11 outliers final: 11 residues processed: 65 average time/residue: 0.3492 time to fit residues: 40.3187 Evaluate side-chains 64 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 53 time to evaluate : 2.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 258 optimal weight: 5.9990 chunk 268 optimal weight: 0.9990 chunk 189 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 278 optimal weight: 0.1980 chunk 196 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 94 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 chunk 211 optimal weight: 4.9990 overall best weight: 2.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.085606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.056174 restraints weight = 80283.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.057928 restraints weight = 45226.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.059091 restraints weight = 32072.525| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 25756 Z= 0.150 Angle : 0.505 10.640 35123 Z= 0.256 Chirality : 0.045 0.417 4083 Planarity : 0.003 0.043 4454 Dihedral : 5.123 54.220 4159 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.40 % Allowed : 8.47 % Favored : 91.12 % 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: 0.33 (0.15), residues: 3098 helix: 2.30 (0.20), residues: 713 sheet: 0.14 (0.19), residues: 664 loop : -0.65 (0.15), residues: 1721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 64 HIS 0.005 0.001 HIS B 954 PHE 0.014 0.001 PHE B 833 TYR 0.022 0.001 TYR B1067 ARG 0.003 0.000 ARG C 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00378 ( 31) link_NAG-ASN : angle 2.31409 ( 93) link_BETA1-4 : bond 0.00765 ( 6) link_BETA1-4 : angle 2.31371 ( 18) link_ALPHA1-3 : bond 0.00587 ( 1) link_ALPHA1-3 : angle 1.40854 ( 3) hydrogen bonds : bond 0.04188 ( 1041) hydrogen bonds : angle 4.79580 ( 2892) SS BOND : bond 0.00245 ( 42) SS BOND : angle 0.56539 ( 84) covalent geometry : bond 0.00356 (25676) covalent geometry : angle 0.48806 (34925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6196 Ramachandran restraints generated. 3098 Oldfield, 0 Emsley, 3098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 3.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.5497 (p90) cc_final: 0.5030 (p90) REVERT: B 1141 LEU cc_start: 0.8831 (tp) cc_final: 0.8611 (tt) REVERT: C 428 ASP cc_start: 0.8585 (m-30) cc_final: 0.8374 (t70) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.3512 time to fit residues: 40.6831 Evaluate side-chains 62 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 52 time to evaluate : 3.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 633 TRP Chi-restraints excluded: chain C residue 353 TRP Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 977 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 10 optimal weight: 0.9980 chunk 250 optimal weight: 9.9990 chunk 277 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 154 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 chunk 182 optimal weight: 7.9990 chunk 253 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 309 optimal weight: 0.2980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 901 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.086859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.057558 restraints weight = 79741.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059417 restraints weight = 44625.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.060600 restraints weight = 31250.345| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 25756 Z= 0.089 Angle : 0.470 10.329 35123 Z= 0.239 Chirality : 0.044 0.390 4083 Planarity : 0.003 0.043 4454 Dihedral : 4.918 54.701 4159 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 0.40 % Allowed : 8.55 % Favored : 91.05 % 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: 0.54 (0.15), residues: 3098 helix: 2.60 (0.20), residues: 702 sheet: 0.25 (0.19), residues: 663 loop : -0.54 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 64 HIS 0.003 0.000 HIS B 954 PHE 0.017 0.001 PHE B 168 TYR 0.019 0.001 TYR B1067 ARG 0.002 0.000 ARG B 905 Details of bonding type rmsd link_NAG-ASN : bond 0.00406 ( 31) link_NAG-ASN : angle 2.18152 ( 93) link_BETA1-4 : bond 0.00770 ( 6) link_BETA1-4 : angle 2.23981 ( 18) link_ALPHA1-3 : bond 0.00638 ( 1) link_ALPHA1-3 : angle 1.34006 ( 3) hydrogen bonds : bond 0.03523 ( 1041) hydrogen bonds : angle 4.60436 ( 2892) SS BOND : bond 0.00156 ( 42) SS BOND : angle 0.49381 ( 84) covalent geometry : bond 0.00194 (25676) covalent geometry : angle 0.45402 (34925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7795.46 seconds wall clock time: 142 minutes 39.95 seconds (8559.95 seconds total)