Starting phenix.real_space_refine on Sun Jul 5 04:00:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tl1_25983/07_2026/7tl1_25983.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tl1_25983/07_2026/7tl1_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7tl1_25983/07_2026/7tl1_25983.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tl1_25983/07_2026/7tl1_25983.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tl1_25983/07_2026/7tl1_25983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tl1_25983/07_2026/7tl1_25983.map" model { file = "/net/cci-nas-00/data/ceres_data/7tl1_25983/07_2026/7tl1_25983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tl1_25983/07_2026/7tl1_25983.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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 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 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 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 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 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 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 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 chiralities: 9 Time building chain proxies: 5.26, per 1000 atoms: 0.21 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: 2.13 Conformation dependent library (CDL) restraints added in 919.3 milliseconds 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: 1.13 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: 6.37 Time building geometry restraints manager: 2.76 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 - 17.75: 14052 17.75 - 35.49: 829 35.49 - 53.24: 104 53.24 - 70.99: 13 70.99 - 88.73: 13 Dihedral angle restraints: 15011 sinusoidal: 5860 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 15008 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 1208)) selection = (chain 'B' and (resid 27 through 844 or resid 850 through 1208)) selection = (chain 'C' and (resid 27 through 210 or resid 219 through 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: 2.230 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: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 23.730 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 : 11.214 88.735 8993 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.005 0.000 ARG A 905 TYR 0.033 0.002 TYR B 837 PHE 0.025 0.002 PHE B 833 TRP 0.015 0.001 TRP A 633 HIS 0.022 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.21 (25676) covalent geometry : angle 0.69175 / 0.38 (34925) SS BOND : bond 0.00228 / 0.15 ( 42) SS BOND : angle 1.12476 / 0.75 ( 84) hydrogen bonds : bond 0.07585 / 4.84 ( 1041) hydrogen bonds : angle 5.71619 / 3.93 ( 2892) link_ALPHA1-3 : bond 0.00494 / 0.26 ( 1) link_ALPHA1-3 : angle 1.25093 / 0.59 ( 3) link_BETA1-4 : bond 0.01059 / 0.76 ( 6) link_BETA1-4 : angle 3.74879 / 1.90 ( 18) link_NAG-ASN : bond 0.00575 / 0.34 ( 31) link_NAG-ASN : angle 4.01857 / 2.75 ( 93) *********************** 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 : 0.750 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: 0.1703 time to fit residues: 21.3626 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 : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 0.4980 chunk 155 optimal weight: 7.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 7.9990 chunk 298 optimal weight: 7.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3729 r_free = 0.3729 target = 0.085868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.056791 restraints weight = 80724.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.058340 restraints weight = 47969.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.058829 restraints weight = 33662.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059170 restraints weight = 30779.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059245 restraints weight = 30111.441| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 25756 Z= 0.221 Angle : 0.579 11.779 35123 Z= 0.296 Chirality : 0.047 0.454 4083 Planarity : 0.004 0.048 4454 Dihedral : 4.380 18.815 3365 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.26 % Allowed : 3.32 % Favored : 96.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.15), residues: 3098 helix: 1.29 (0.19), residues: 712 sheet: 0.22 (0.19), residues: 663 loop : -0.80 (0.14), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 634 TYR 0.022 0.002 TYR B1067 PHE 0.026 0.002 PHE A 906 TRP 0.009 0.001 TRP B 886 HIS 0.009 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00523 / 0.22 (25676) covalent geometry : angle 0.55859 / 0.29 (34925) SS BOND : bond 0.00371 / 0.29 ( 42) SS BOND : angle 0.84858 / 0.56 ( 84) hydrogen bonds : bond 0.04895 / 3.15 ( 1041) hydrogen bonds : angle 5.10729 / 3.53 ( 2892) link_ALPHA1-3 : bond 0.00138 / 0.07 ( 1) link_ALPHA1-3 : angle 1.80074 / 0.99 ( 3) link_BETA1-4 : bond 0.00828 / 0.57 ( 6) link_BETA1-4 : angle 2.39250 / 1.26 ( 18) link_NAG-ASN : bond 0.00523 / 0.32 ( 31) link_NAG-ASN : angle 2.72810 / 1.87 ( 93) *********************** 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 : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.5022 (p90) cc_final: 0.4767 (p90) outliers start: 7 outliers final: 2 residues processed: 64 average time/residue: 0.1790 time to fit residues: 19.0713 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 : 1.148 ------------------------------------------------------------------------------- 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 300 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 289 optimal weight: 0.7980 chunk 97 optimal weight: 0.3980 chunk 127 optimal weight: 2.9990 chunk 267 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 176 optimal weight: 0.9980 chunk 67 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.086979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.058092 restraints weight = 80475.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059703 restraints weight = 46823.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.060061 restraints weight = 32082.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.060189 restraints weight = 36001.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.060317 restraints weight = 29887.323| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 25756 Z= 0.105 Angle : 0.485 11.364 35123 Z= 0.248 Chirality : 0.044 0.408 4083 Planarity : 0.003 0.045 4454 Dihedral : 4.074 19.343 3365 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 0.26 % Allowed : 4.75 % Favored : 95.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.15), residues: 3098 helix: 1.85 (0.20), residues: 713 sheet: 0.30 (0.19), residues: 656 loop : -0.68 (0.15), residues: 1729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 634 TYR 0.021 0.001 TYR B1067 PHE 0.020 0.001 PHE B 338 TRP 0.007 0.001 TRP B 886 HIS 0.008 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (25676) covalent geometry : angle 0.46653 / 0.24 (34925) SS BOND : bond 0.00190 / 0.14 ( 42) SS BOND : angle 0.58471 / 0.39 ( 84) hydrogen bonds : bond 0.03941 / 2.52 ( 1041) hydrogen bonds : angle 4.83882 / 3.33 ( 2892) link_ALPHA1-3 : bond 0.00521 / 0.27 ( 1) link_ALPHA1-3 : angle 1.39038 / 0.76 ( 3) link_BETA1-4 : bond 0.00823 / 0.61 ( 6) link_BETA1-4 : angle 2.14371 / 1.14 ( 18) link_NAG-ASN : bond 0.00425 / 0.25 ( 31) link_NAG-ASN : angle 2.44152 / 1.70 ( 93) *********************** 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: 7 poor density : 56 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.4837 (p90) cc_final: 0.4516 (p90) REVERT: C 428 ASP cc_start: 0.8650 (m-30) cc_final: 0.8446 (t70) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.1569 time to fit residues: 16.7087 Evaluate side-chains 57 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 241 optimal weight: 20.0000 chunk 84 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 11 optimal weight: 20.0000 chunk 113 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 36 optimal weight: 40.0000 chunk 32 optimal weight: 0.1980 chunk 124 optimal weight: 2.9990 chunk 239 optimal weight: 10.0000 chunk 159 optimal weight: 0.7980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 448 ASN C 965 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.084949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.055802 restraints weight = 80459.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.057599 restraints weight = 47983.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057952 restraints weight = 31779.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058544 restraints weight = 29237.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058562 restraints weight = 27904.937| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.1503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 25756 Z= 0.237 Angle : 0.576 10.914 35123 Z= 0.295 Chirality : 0.047 0.435 4083 Planarity : 0.004 0.045 4454 Dihedral : 4.301 20.535 3365 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.47 % Allowed : 6.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.01 (0.15), residues: 3098 helix: 1.72 (0.20), residues: 719 sheet: 0.10 (0.19), residues: 665 loop : -0.77 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 905 TYR 0.024 0.002 TYR B1067 PHE 0.020 0.002 PHE A 906 TRP 0.008 0.001 TRP B 353 HIS 0.008 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (25676) covalent geometry : angle 0.55957 / 0.29 (34925) SS BOND : bond 0.00377 / 0.29 ( 42) SS BOND : angle 0.70355 / 0.46 ( 84) hydrogen bonds : bond 0.05062 / 3.25 ( 1041) hydrogen bonds : angle 5.07729 / 3.51 ( 2892) link_ALPHA1-3 : bond 0.00345 / 0.18 ( 1) link_ALPHA1-3 : angle 1.48621 / 0.74 ( 3) link_BETA1-4 : bond 0.00731 / 0.55 ( 6) link_BETA1-4 : angle 2.24612 / 1.18 ( 18) link_NAG-ASN : bond 0.00442 / 0.28 ( 31) link_NAG-ASN : angle 2.49542 / 1.74 ( 93) *********************** 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: 13 poor density : 56 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 456 PHE cc_start: 0.5016 (p90) cc_final: 0.4526 (p90) outliers start: 13 outliers final: 7 residues processed: 65 average time/residue: 0.1493 time to fit residues: 16.7955 Evaluate side-chains 57 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1104 VAL Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain C residue 369 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 156 optimal weight: 6.9990 chunk 82 optimal weight: 1.9990 chunk 177 optimal weight: 4.9990 chunk 242 optimal weight: 8.9990 chunk 56 optimal weight: 3.9990 chunk 190 optimal weight: 0.7980 chunk 107 optimal weight: 8.9990 chunk 69 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 76 optimal weight: 0.0670 chunk 252 optimal weight: 9.9990 overall best weight: 1.5322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN C 580 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.086222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.057329 restraints weight = 79826.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058802 restraints weight = 46856.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059364 restraints weight = 32746.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.059476 restraints weight = 34739.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.059567 restraints weight = 29646.648| |-----------------------------------------------------------------------------| r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25756 Z= 0.112 Angle : 0.485 10.677 35123 Z= 0.247 Chirality : 0.044 0.389 4083 Planarity : 0.003 0.044 4454 Dihedral : 4.036 20.079 3365 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 0.33 % Allowed : 7.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.15), residues: 3098 helix: 2.18 (0.20), residues: 707 sheet: 0.21 (0.19), residues: 658 loop : -0.67 (0.15), residues: 1733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 905 TYR 0.020 0.001 TYR B1067 PHE 0.022 0.001 PHE B 338 TRP 0.006 0.001 TRP B 886 HIS 0.006 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.11 (25676) covalent geometry : angle 0.46793 / 0.24 (34925) SS BOND : bond 0.00197 / 0.14 ( 42) SS BOND : angle 0.54723 / 0.37 ( 84) hydrogen bonds : bond 0.04010 / 2.57 ( 1041) hydrogen bonds : angle 4.81656 / 3.32 ( 2892) link_ALPHA1-3 : bond 0.00482 / 0.25 ( 1) link_ALPHA1-3 : angle 1.36129 / 0.72 ( 3) link_BETA1-4 : bond 0.00783 / 0.59 ( 6) link_BETA1-4 : angle 2.08561 / 1.10 ( 18) link_NAG-ASN : bond 0.00398 / 0.24 ( 31) link_NAG-ASN : angle 2.29981 / 1.61 ( 93) *********************** 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 64 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7954 (t80) cc_final: 0.7528 (t80) REVERT: B 456 PHE cc_start: 0.5008 (p90) cc_final: 0.4532 (p90) outliers start: 9 outliers final: 7 residues processed: 62 average time/residue: 0.1341 time to fit residues: 14.9931 Evaluate side-chains 59 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.868 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 9 optimal weight: 8.9990 chunk 163 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 268 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 130 optimal weight: 7.9990 chunk 301 optimal weight: 4.9990 chunk 286 optimal weight: 5.9990 chunk 151 optimal weight: 20.0000 chunk 97 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.085083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.055479 restraints weight = 80361.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.057253 restraints weight = 45633.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.058398 restraints weight = 32384.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.059082 restraints weight = 26488.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059509 restraints weight = 23576.902| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 25756 Z= 0.199 Angle : 0.537 10.612 35123 Z= 0.274 Chirality : 0.046 0.415 4083 Planarity : 0.003 0.044 4454 Dihedral : 4.142 19.945 3365 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 0.47 % Allowed : 7.71 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.15), residues: 3098 helix: 2.03 (0.20), residues: 713 sheet: 0.12 (0.19), residues: 658 loop : -0.73 (0.14), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.023 0.001 TYR B1067 PHE 0.015 0.001 PHE B 833 TRP 0.007 0.001 TRP B 353 HIS 0.006 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.20 (25676) covalent geometry : angle 0.52130 / 0.27 (34925) SS BOND : bond 0.00308 / 0.24 ( 42) SS BOND : angle 0.61974 / 0.41 ( 84) hydrogen bonds : bond 0.04605 / 2.96 ( 1041) hydrogen bonds : angle 4.94310 / 3.42 ( 2892) link_ALPHA1-3 : bond 0.00387 / 0.20 ( 1) link_ALPHA1-3 : angle 1.44215 / 0.72 ( 3) link_BETA1-4 : bond 0.00715 / 0.54 ( 6) link_BETA1-4 : angle 2.20636 / 1.16 ( 18) link_NAG-ASN : bond 0.00411 / 0.26 ( 31) link_NAG-ASN : angle 2.38423 / 1.66 ( 93) *********************** 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: 13 poor density : 54 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7873 (t80) cc_final: 0.7453 (t80) REVERT: A 934 ILE cc_start: 0.9143 (OUTLIER) cc_final: 0.8936 (tt) REVERT: B 456 PHE cc_start: 0.5324 (p90) cc_final: 0.4884 (p90) outliers start: 13 outliers final: 8 residues processed: 65 average time/residue: 0.1457 time to fit residues: 16.5375 Evaluate side-chains 62 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 993 ILE Chi-restraints excluded: chain A residue 1050 MET Chi-restraints excluded: chain A residue 1098 ASN 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 C residue 977 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 103 optimal weight: 3.9990 chunk 217 optimal weight: 7.9990 chunk 2 optimal weight: 8.9990 chunk 108 optimal weight: 5.9990 chunk 279 optimal weight: 0.6980 chunk 297 optimal weight: 6.9990 chunk 233 optimal weight: 0.3980 chunk 260 optimal weight: 0.2980 chunk 280 optimal weight: 6.9990 chunk 91 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.086094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.056989 restraints weight = 79744.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058705 restraints weight = 46293.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059583 restraints weight = 31106.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.059633 restraints weight = 29083.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.059801 restraints weight = 27031.142| |-----------------------------------------------------------------------------| r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.1567 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= 0.113 Angle : 0.493 13.337 35123 Z= 0.249 Chirality : 0.044 0.385 4083 Planarity : 0.003 0.043 4454 Dihedral : 4.001 25.327 3365 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.55 % Allowed : 8.04 % Favored : 91.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.15), residues: 3098 helix: 2.31 (0.20), residues: 707 sheet: 0.13 (0.19), residues: 671 loop : -0.67 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 905 TYR 0.020 0.001 TYR B1067 PHE 0.012 0.001 PHE B 833 TRP 0.005 0.001 TRP B 886 HIS 0.005 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (25676) covalent geometry : angle 0.47760 / 0.25 (34925) SS BOND : bond 0.00196 / 0.14 ( 42) SS BOND : angle 0.53678 / 0.37 ( 84) hydrogen bonds : bond 0.03946 / 2.53 ( 1041) hydrogen bonds : angle 4.77157 / 3.29 ( 2892) link_ALPHA1-3 : bond 0.00454 / 0.24 ( 1) link_ALPHA1-3 : angle 1.37442 / 0.71 ( 3) link_BETA1-4 : bond 0.00765 / 0.57 ( 6) link_BETA1-4 : angle 2.10250 / 1.10 ( 18) link_NAG-ASN : bond 0.00392 / 0.24 ( 31) link_NAG-ASN : angle 2.25814 / 1.58 ( 93) *********************** 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: 15 poor density : 54 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7898 (t80) cc_final: 0.7460 (t80) REVERT: A 934 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8853 (tt) REVERT: B 456 PHE cc_start: 0.5296 (p90) cc_final: 0.4928 (p90) outliers start: 15 outliers final: 8 residues processed: 66 average time/residue: 0.1479 time to fit residues: 17.1020 Evaluate side-chains 62 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 934 ILE 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 244 optimal weight: 0.0970 chunk 93 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 204 optimal weight: 2.9990 chunk 136 optimal weight: 20.0000 chunk 1 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 207 optimal weight: 7.9990 chunk 162 optimal weight: 4.9990 chunk 305 optimal weight: 4.9990 chunk 201 optimal weight: 4.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.085550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.056491 restraints weight = 80246.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.058186 restraints weight = 47951.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.058819 restraints weight = 32278.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.058789 restraints weight = 30501.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.058984 restraints weight = 30042.845| |-----------------------------------------------------------------------------| r_work (final): 0.3070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.1685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 25756 Z= 0.158 Angle : 0.513 11.335 35123 Z= 0.261 Chirality : 0.045 0.399 4083 Planarity : 0.003 0.044 4454 Dihedral : 4.031 21.107 3365 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.47 % Allowed : 8.44 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3098 helix: 2.23 (0.20), residues: 713 sheet: 0.13 (0.19), residues: 665 loop : -0.69 (0.15), residues: 1720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 905 TYR 0.021 0.001 TYR B1067 PHE 0.014 0.001 PHE B 833 TRP 0.012 0.001 TRP A 64 HIS 0.005 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 (25676) covalent geometry : angle 0.49696 / 0.26 (34925) SS BOND : bond 0.00267 / 0.20 ( 42) SS BOND : angle 0.68639 / 0.44 ( 84) hydrogen bonds : bond 0.04255 / 2.73 ( 1041) hydrogen bonds : angle 4.82398 / 3.33 ( 2892) link_ALPHA1-3 : bond 0.00411 / 0.22 ( 1) link_ALPHA1-3 : angle 1.41535 / 0.71 ( 3) link_BETA1-4 : bond 0.00738 / 0.55 ( 6) link_BETA1-4 : angle 2.15001 / 1.12 ( 18) link_NAG-ASN : bond 0.00391 / 0.24 ( 31) link_NAG-ASN : angle 2.30812 / 1.61 ( 93) *********************** 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 70 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7894 (t80) cc_final: 0.7485 (t80) REVERT: A 934 ILE cc_start: 0.9090 (OUTLIER) cc_final: 0.8879 (tt) REVERT: B 456 PHE cc_start: 0.5359 (p90) cc_final: 0.4978 (p90) outliers start: 13 outliers final: 10 residues processed: 69 average time/residue: 0.1440 time to fit residues: 17.6593 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 : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 934 ILE 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 C residue 353 TRP Chi-restraints excluded: chain C residue 369 TYR Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 934 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 101 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 150 optimal weight: 20.0000 chunk 57 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 223 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 chunk 215 optimal weight: 6.9990 chunk 236 optimal weight: 0.9990 chunk 244 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN B1135 ASN C 448 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.086827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.057832 restraints weight = 80406.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.060094 restraints weight = 46639.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.060160 restraints weight = 29627.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.060564 restraints weight = 28548.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.060669 restraints weight = 27623.111| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1605 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 : 0.473 11.144 35123 Z= 0.239 Chirality : 0.044 0.370 4083 Planarity : 0.003 0.043 4454 Dihedral : 3.827 18.001 3365 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.40 % Allowed : 8.51 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3098 helix: 2.47 (0.20), residues: 708 sheet: 0.22 (0.19), residues: 662 loop : -0.58 (0.15), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 905 TYR 0.019 0.001 TYR B1067 PHE 0.012 0.001 PHE B 833 TRP 0.018 0.001 TRP A 64 HIS 0.004 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (25676) covalent geometry : angle 0.45736 / 0.24 (34925) SS BOND : bond 0.00172 / 0.12 ( 42) SS BOND : angle 0.55611 / 0.36 ( 84) hydrogen bonds : bond 0.03544 / 2.28 ( 1041) hydrogen bonds : angle 4.63298 / 3.19 ( 2892) link_ALPHA1-3 : bond 0.00482 / 0.25 ( 1) link_ALPHA1-3 : angle 1.34017 / 0.70 ( 3) link_BETA1-4 : bond 0.00749 / 0.55 ( 6) link_BETA1-4 : angle 2.06247 / 1.08 ( 18) link_NAG-ASN : bond 0.00409 / 0.24 ( 31) link_NAG-ASN : angle 2.17178 / 1.52 ( 93) *********************** 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 70 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7956 (t80) cc_final: 0.7542 (t80) REVERT: B 456 PHE cc_start: 0.5263 (p90) cc_final: 0.4833 (p90) REVERT: C 1050 MET cc_start: 0.8111 (mtt) cc_final: 0.7806 (mtt) outliers start: 11 outliers final: 9 residues processed: 67 average time/residue: 0.1563 time to fit residues: 17.8807 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 : 0.941 ------------------------------------------------------------------------------- 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 313 random chunks: chunk 274 optimal weight: 4.9990 chunk 189 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 196 optimal weight: 4.9990 chunk 281 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 126 optimal weight: 5.9990 chunk 279 optimal weight: 0.0060 chunk 22 optimal weight: 0.9980 chunk 252 optimal weight: 9.9990 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 580 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.084987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.055447 restraints weight = 80434.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.057198 restraints weight = 45795.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.058338 restraints weight = 32677.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.059030 restraints weight = 26751.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.059359 restraints weight = 23844.206| |-----------------------------------------------------------------------------| r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 25756 Z= 0.207 Angle : 0.550 11.165 35123 Z= 0.279 Chirality : 0.046 0.414 4083 Planarity : 0.003 0.044 4454 Dihedral : 4.074 19.460 3365 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.47 % Allowed : 8.62 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.27 (0.15), residues: 3098 helix: 2.24 (0.20), residues: 708 sheet: 0.14 (0.19), residues: 660 loop : -0.69 (0.15), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 905 TYR 0.022 0.001 TYR B1067 PHE 0.015 0.001 PHE B 833 TRP 0.015 0.001 TRP A 64 HIS 0.006 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00494 / 0.21 (25676) covalent geometry : angle 0.53477 / 0.28 (34925) SS BOND : bond 0.00328 / 0.25 ( 42) SS BOND : angle 0.65634 / 0.42 ( 84) hydrogen bonds : bond 0.04625 / 2.97 ( 1041) hydrogen bonds : angle 4.89011 / 3.38 ( 2892) link_ALPHA1-3 : bond 0.00365 / 0.19 ( 1) link_ALPHA1-3 : angle 1.45440 / 0.71 ( 3) link_BETA1-4 : bond 0.00736 / 0.55 ( 6) link_BETA1-4 : angle 2.24290 / 1.17 ( 18) link_NAG-ASN : bond 0.00409 / 0.26 ( 31) link_NAG-ASN : angle 2.32950 / 1.63 ( 93) ********************** 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 66 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 375 PHE cc_start: 0.7843 (t80) cc_final: 0.7471 (t80) REVERT: B 456 PHE cc_start: 0.5491 (p90) cc_final: 0.5050 (p90) outliers start: 13 outliers final: 10 residues processed: 64 average time/residue: 0.1468 time to fit residues: 16.4740 Evaluate side-chains 61 residues out of total 2738 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 51 time to evaluate : 0.950 ------------------------------------------------------------------------------- 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 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 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 146 optimal weight: 10.0000 chunk 291 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 145 optimal weight: 8.9990 chunk 47 optimal weight: 10.0000 chunk 298 optimal weight: 1.9990 chunk 90 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 chunk 236 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.086534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.057774 restraints weight = 80160.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.059650 restraints weight = 47842.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.059818 restraints weight = 31154.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.060156 restraints weight = 31709.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.060232 restraints weight = 30186.980| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 25756 Z= 0.102 Angle : 0.486 10.626 35123 Z= 0.245 Chirality : 0.044 0.375 4083 Planarity : 0.003 0.043 4454 Dihedral : 3.868 18.666 3365 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.33 % Allowed : 8.77 % Favored : 90.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.46 (0.15), residues: 3098 helix: 2.53 (0.20), residues: 701 sheet: 0.23 (0.19), residues: 662 loop : -0.60 (0.15), residues: 1735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 905 TYR 0.020 0.001 TYR B1067 PHE 0.012 0.001 PHE B 833 TRP 0.015 0.001 TRP A 64 HIS 0.004 0.001 HIS B 954 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (25676) covalent geometry : angle 0.47096 / 0.24 (34925) SS BOND : bond 0.00176 / 0.12 ( 42) SS BOND : angle 0.54669 / 0.36 ( 84) hydrogen bonds : bond 0.03701 / 2.38 ( 1041) hydrogen bonds : angle 4.67717 / 3.22 ( 2892) link_ALPHA1-3 : bond 0.00464 / 0.24 ( 1) link_ALPHA1-3 : angle 1.32342 / 0.69 ( 3) link_BETA1-4 : bond 0.00718 / 0.52 ( 6) link_BETA1-4 : angle 2.07133 / 1.09 ( 18) link_NAG-ASN : bond 0.00402 / 0.24 ( 31) link_NAG-ASN : angle 2.17799 / 1.53 ( 93) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3412.73 seconds wall clock time: 60 minutes 10.06 seconds (3610.06 seconds total)